Setup

1. Uva reef

Import Coral cover data

(Wide format)

# Read data 
  cover <- read.csv("CoverData/Uva_cover_R1.csv", header=TRUE, sep = ",")
  #summary(cover)
  
# Convert variables and factors to right format
  # convert to numeric variables
  cover$Pocillopora <- as.numeric(cover$Pocillopora) 
  cover$Massive <- as.numeric(cover$Other_scleractinians)
  cover$Millepora <- as.numeric(cover$Millepora) 
  cover$Algae<- as.numeric(cover$Algae)
  cover$Substrate<- as.numeric(cover$Substrate)
  cover$YEAR <- as.numeric(cover$YEAR)
  # convert to nominal factors
  cover$Location <- as.factor(cover$Location) 

# Dates   
  # Note: all day from a month were converted to the 15th  
  cover$Date<-as.Date(cover$Date, format =  "%Y-%m-%d")

  #summary(cover)
  str(cover)
## 'data.frame':    539 obs. of  112 variables:
##  $ YEAR                                   : num  1980 1980 1980 1980 1980 1980 1980 1980 1980 1980 ...
##  $ Month                                  : Factor w/ 12 levels "Apr","Aug","Dec",..: 3 3 3 3 3 3 3 3 3 3 ...
##  $ Location                               : Factor w/ 3 levels "4x5","Uva_1m2",..: 3 3 3 3 3 3 3 3 3 3 ...
##  $ Transect                               : Factor w/ 12 levels "4x5","I","II",..: 2 3 4 5 6 7 8 9 10 11 ...
##  $ Date.of.Data.Collection.               : Factor w/ 76 levels "01/01/85","01/01/94",..: 75 75 75 75 75 75 75 75 75 75 ...
##  $ Date                                   : Date, format: "1980-12-15" "1980-12-15" ...
##  $ Depth.m.                               : int  2 2 2 2 2 2 2 2 2 2 ...
##  $ X.of.benth.points                      : int  NA NA NA NA NA NA NA NA NA NA ...
##  $ X.of.subst.points                      : int  NA NA NA NA NA NA NA NA NA NA ...
##  $ Analysis.by                            : Factor w/ 9 levels "","?","Peggy Fong",..: 4 4 4 4 4 4 4 4 4 4 ...
##  $ Date.of.Analysis                       : Factor w/ 9 levels "","04/04/17",..: NA NA NA NA NA NA NA NA NA NA ...
##  $ Processing                             : Factor w/ 7 levels "CPCe over Image",..: 6 6 6 6 6 6 6 6 6 6 ...
##  $ Transect.Type                          : Factor w/ 4 levels "Estimated","Permanent",..: 3 3 3 3 3 3 3 3 3 3 ...
##  $ Method                                 : Factor w/ 3 levels "Chain_Transect",..: 1 1 1 1 1 1 1 1 1 1 ...
##  $ Cycloceris.curvata..CCUR....coral      : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Diaseris.distorta..DDIS....coral       : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Gardineroseris.planulata..GPLA....coral: num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Gpla_BL                                : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Leptoseris.scabra..LSCA....coral       : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Pavona.chiriquiensis..PCHI....coral    : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Pavona.clavus..PCLA....coral           : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Pavona.gigantea..PGIG....coral         : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Pgig_BL                                : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Pavona.maldivensis..PMAL....coral      : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Pavona.varians..PVAR....coral          : num  0 0 0 0 0 ...
##  $ Pvar_BL                                : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Pvar_Pale                              : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Pavona.spp..PAVO....coral              : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Porites.lobata..PLOB....coral          : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Porites.panamensis..PPAN....coral      : num  0.137 0.137 0 0 0 ...
##  $ Ppan_BL                                : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Psammocora.stellata..PSTE....coral     : num  0 0 0 0 0 ...
##  $ Psammocora.superficialis..PSUP....coral: num  0 0 0 0 0 ...
##  $ Psammocora.spp..PSAM....coral          : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Pocillopora.capitata..PCAP....coral    : num  3.288 0.959 9.178 4.11 0 ...
##  $ Pocillopora.damicornis..PDAM....coral  : num  3.151 2.603 0.411 2.877 1.781 ...
##  $ Pdam_BL                                : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Pdam_Pale                              : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Pocillopora.effusus..PEFF....coral     : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Pocillopora.elegans..PELE....coral     : num  17.4 0 0 0 0 ...
##  $ Pele_BL                                : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Pele_Pale                              : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Pocillopora.eydouxi..PEYD....coral     : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Pocillopora.inflata..PINF....coral     : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Pocillopora.ligulata..PLIG....coral    : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Pocillopora.meandrina..PMEA....coral   : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Pocillopora.verrucosa..PVER....coral   : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Pocillopora.woodjonesi..PWOO....coral  : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Pocillopora.spp..POCI....coral         : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ RecMort                                : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Millepora.intricata..MINT....coral     : num  0 0 0 3.97 0 ...
##  $ Mint_BL                                : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Millepora.platyphilla..MPLA....coral   : num  3.97 0 0 0 0 ...
##  $ Mpla_BL                                : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Astrangia.browni..ABRO....aherm        : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Astrangia.equatorialis..AEQU....aherm  : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Caryophyllia.sp...CARYSPP....aherm     : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Cladopsammia.eguchii..CEGU....aherm    : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Cladopsammia.gracilis..CGRA....aherm   : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Culicia.stellata..CSTE....aherm        : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Oulangia.bradleyi..OBRA....aherm       : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Phyllangia.consagensis..PCON....aherm  : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Polycyathus.isabela..PISA....aherm     : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Rhizopsammia.verrilli..RVER....aherm   : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Rhizopsammia.wellingtoni..RWEL....aherm: int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Tubastraea.coccinea..TCOC....aherm     : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Tubastraea.faulkneri..TFAU....aherm    : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Tubastraea.floreana..TFLO....aherm     : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Tubastraea.tagusensis..TTAG....aherm   : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ BLCHCoral                              : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Coral..C.                              : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Gorgonian..GO....go                    : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Zoanthids..ZO....zo                    : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Sponge..SPO....spo                     : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Antipathes.galapagensis..AGAL....bcoral: int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Myriopathes.panamensis..MPAN....bcoral : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Balanus..BALA....O                     : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Algmt                                  : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ AlgRub                                 : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Caulerpa..CAUL....maca                 : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Caulerpa_Feather.CSER.                 : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Caulerpa_Grape.CRAC.                   : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Coralline.Algae..CALG....calg          : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Filamentous.Cyanobacteria..FLCY....maca: num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Laurencia                              : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Macroalgae..MACA....maca               : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Peysonnelia                            : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Turf                                   : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Other.Organism..O.                     : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Dead.coral.w..turf.algae..DCA....dca   : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Dead.Frame                             : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ DAMFR                                  : num  NA NA NA NA NA NA NA NA NA NA ...
##  $ Boulder..B.                            : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Sand.Sediment..S.                      : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Rubble..R.                             : num  72.1 96.3 90.4 89 98.2 ...
##  $ Pavement..P.                           : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ Unknown..UNK.                          : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ NA.LOSS                                : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ Tape.edge                              : num  0 0 0 0 0 0 0 0 0 0 ...
##   [list output truncated]

Check transects/sample units

Explore data

Pocillopora

  • Pre-1982 Pocillopora cover in 4*5 = 77% manually added
  • Line = mean
  • Boxplots = median

Non-Pocillopora scleractinians (Uva)

  • Line = mean
  • Boxplots = median

Millepora (Uva)

  • Millepora spp. (individual transects)

Data analysis (Aggregated data)

Aggregate data (Pocillopora)

  • Hierarchically aggregate by date and location
# Aggregate by Dataset - Month -Year
  aggr.location <- aggregate(Pocillopora 
                             ~YEAR+Month+Location,
                             FUN=mean, data=cover)
  
  aggr.location$Year_F<-as.factor(aggr.location$YEAR)
  aggr.location$Date<-paste(aggr.location$YEAR, aggr.location$Month, "15", sep = "-")
  aggr.location$Date<-as.Date(aggr.location$Date, format = "%Y-%b-%d")
  str(aggr.location)
## 'data.frame':    88 obs. of  6 variables:
##  $ YEAR       : num  2016 2017 1984 1985 2014 ...
##  $ Month      : Factor w/ 12 levels "Apr","Aug","Dec",..: 1 1 2 2 2 2 2 3 3 3 ...
##  $ Location   : Factor w/ 3 levels "4x5","Uva_1m2",..: 1 1 1 1 1 1 1 1 1 1 ...
##  $ Pocillopora: num  57.28 71.659 0.242 0.62 73.07 ...
##  $ Year_F     : Factor w/ 29 levels "1980","1983",..: 27 28 3 4 25 26 29 1 3 9 ...
##  $ Date       : Date, format: "2016-04-15" "2017-04-15" ...
  #write.csv(aggr.location, 
   #       "Outputs/Pocillopora_mean_by_dataset.csv",
   #       row.names = F)

Stats Pocillopora for conceptual model (pooled datasets)

Pocillopora (model 0)

This model includes aggregated data from Chiriqui

  • Aggregated by location (Dataset)
  • YEAR is a continuous variable
  • Location (Dataset) as a random factor

  • Model is significant, but ignores high cover pre-1982

  • Data does not look normally distributed, which is ok, since the coral cover cannot be linear (Year as continuous), unless pre-1982 is removed?

** Do I need to change the intercept options?**

# # All years 1980_2018 
#   model0 <- lme(
#     Pocillopora ~ -1 + YEAR, random = ~1|Location, data=aggr.location)
#   summary(model0)
#   anova(model0)
#   
#   plot(ranef(model0))    # Symmetrical scatter effects around zero?
#   plot(model0)           # plot residuals vs fitted
#   resnorm1 <- resid(model0)
#   hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
#   coef.m1 <- as.data.frame(coef(summary(model0)))    # Coefficients of the model
#   
#   plot(model0, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
#   plot(model0, Pocillopora ~ fitted(.), abline = c(0,1))

#-----
  model0 <- lme(
  Pocillopora ~ YEAR, random = ~1|Location, data=aggr.location)
  summary(model0)
## Linear mixed-effects model fit by REML
##   Data: aggr.location 
##        AIC     BIC    logLik
##   725.0116 734.829 -358.5058
## 
## Random effects:
##  Formula: ~1 | Location
##         (Intercept) Residual
## StdDev:    8.911826 14.02862
## 
## Fixed effects:  Pocillopora ~ YEAR 
##                  Value Std.Error DF   t-value p-value
## (Intercept) -3073.5862 277.08378 84 -11.09262       0
## YEAR            1.5485   0.13859 84  11.17316       0
##  Correlation: 
##      (Intr)
## YEAR -1    
## 
## Standardized Within-Group Residuals:
##        Min         Q1        Med         Q3        Max 
## -1.1964839 -0.5889819 -0.2624917  0.4554009  5.4195389 
## 
## Number of Observations: 88
## Number of Groups: 3
  anova(model0)
  plot(ranef(model0))    # Symmetrical scatter effects around zero?
  plot(model0)           # plot residuals vs fitted
  resnorm1 <- resid(model0)
  hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
  coef.m1 <- as.data.frame(coef(summary(model0)))    # Coefficients of the model
  
  plot(model0, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
  plot(model0, Pocillopora ~ fitted(.), abline = c(0,1))

Model 0 (data) plot vs (predicted values)

Model_0 <- ggplot(aggr.location, aes(x=YEAR, y=Pocillopora)) +
  stat_boxplot(aes(group=YEAR), geom = 'errorbar')+
  geom_point(aes(colour=Location))+
  geom_smooth(method = lm, se=FALSE, linetype = "dashed", colour="red")+
  geom_smooth(span = 0.3, se=T, colour="darkgray")+ 

  scale_y_continuous("Pocillopora cover (%)",
                      breaks = seq(0, 80, by=10),
                     limits = c(-2, 80),
                     expand = c(0,0))+
  scale_x_continuous("", limits = c(1979, 2019),
                     breaks = seq(1980, 2018, by=2),
                     expand = c(0,0))+
  annotate("rect", xmin = 1982, xmax = 1983, 
           ymin = 0, ymax = 80,  alpha = .2, fill="gray")+
  annotate("rect", xmin = 1997, xmax = 1998, 
           ymin = 0, ymax = 80,  alpha = .2, fill="gray")+
  annotate("rect", xmin = 2015, xmax = 2016,
           ymin = 0, ymax = 80,  alpha = .2, fill="gray")+
  theme(legend.position = c(0.25, 0.8))+
  labs(title="Model 1 data")

Model 0

  • Extract model 1 predicted values
# Create a new data frame for independent variables  
NewData_0 <- expand.grid(Location=unique(aggr.location$Location),
                        YEAR=seq((min(aggr.location$YEAR)), (max(aggr.location$YEAR))))
pred_0 <- predict(model0 , newdata=NewData_0, level=0)
#summary(pred_0) 
#length(pred_0)
  • Plot model predictions
# Using model data 
  Model0_plot <- ggplot(aggr.location, 
                        aes(x=YEAR, y=Pocillopora, colour=Location)) +
      geom_point(aes(fill=factor(Location)),
                 shape = 21, colour = "black",
                 size = 2, stroke = 0.3, alpha=0.5) +
      
  scale_y_continuous("Pocillopora cover (%)", 
                     breaks = seq(0, 80, by=10), 
                     limits = c(-2, 80),
                     expand = c(0 ,0))+
  scale_x_continuous("", limits = c(1979, 2018),
                     breaks = seq(1980, 2018, by=2), 
                     expand = c(0.02,0.02))+
  
  geom_line(data=NewData_0, 
            aes(y=predict(model0, level=0, newdata=NewData_0)), size=2)+
  labs(title="Model 1 prediction")
  • Compare data and predictions
 Model0_All<-grid.arrange(Model_0, Model0_plot, ncol=2)

Pocillopora (model 0b: removing 1980 datapoints)

This model includes aggregated data from Chiriqui

  • Aggregated by location (Dataset)
  • YEAR is a continuous variable (1980 data removed)
  • Location (Dataset) as a random factor
aggr.locationb<-filter(aggr.location, YEAR>1983)
summary(aggr.locationb)
##       YEAR          Month           Location   Pocillopora          Year_F  
##  Min.   :1984   Mar    :22   4x5        :38   Min.   : 0.2145   1985   : 8  
##  1st Qu.:1988   Aug    :12   Uva_1m2    :18   1st Qu.: 1.5079   1984   : 7  
##  Median :1997   Jul    :10   UvRf-Chains:27   Median :12.9349   1997   : 5  
##  Mean   :1999   Feb    : 7                    Mean   :20.6385   1989   : 3  
##  3rd Qu.:2006   Jan    : 7                    3rd Qu.:33.5717   1990   : 3  
##  Max.   :2018   Apr    : 6                    Max.   :73.5546   1994   : 3  
##                 (Other):19                                      (Other):54  
##       Date           
##  Min.   :1984-06-15  
##  1st Qu.:1988-10-15  
##  Median :1997-10-15  
##  Mean   :1999-01-14  
##  3rd Qu.:2006-11-13  
##  Max.   :2018-08-15  
## 
  • Seems that removing the intercept is an issue…
# All years 1980_2018 

  model0b <- lme(
    Pocillopora ~ YEAR, random = ~1| Location, data=aggr.locationb)
  summary(model0b)
## Linear mixed-effects model fit by REML
##   Data: aggr.locationb 
##        AIC      BIC    logLik
##   630.7988 640.3766 -311.3994
## 
## Random effects:
##  Formula: ~1 | Location
##         (Intercept) Residual
## StdDev:    10.05117 9.986885
## 
## Fixed effects:  Pocillopora ~ YEAR 
##                 Value Std.Error DF   t-value p-value
## (Intercept) -3648.888 211.14511 79 -17.28142       0
## YEAR            1.835   0.10554 79  17.38993       0
##  Correlation: 
##      (Intr)
## YEAR -1    
## 
## Standardized Within-Group Residuals:
##        Min         Q1        Med         Q3        Max 
## -1.8626007 -0.5962037 -0.1968177  0.5313649  2.2762352 
## 
## Number of Observations: 83
## Number of Groups: 3
  anova(model0b)
  print(model0b)
## Linear mixed-effects model fit by REML
##   Data: aggr.locationb 
##   Log-restricted-likelihood: -311.3994
##   Fixed: Pocillopora ~ YEAR 
##  (Intercept)         YEAR 
## -3648.888298     1.835369 
## 
## Random effects:
##  Formula: ~1 | Location
##         (Intercept) Residual
## StdDev:    10.05117 9.986885
## 
## Number of Observations: 83
## Number of Groups: 3
  plot(ranef(model0b))    # Symmetrical scatter effects around zero?
  plot(model0b)           # plot residuals vs fitted
  resnorm1 <- resid(model0b)
  hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
  coef.m1 <- as.data.frame(coef(summary(model0b)))    # Coefficients of the model
  
  plot(model0b, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
  plot(model0b, Pocillopora ~ fitted(.), abline = c(0,1))

Model 0b (data) plot

Model 0b

  • Extract model 1b predicted values
# Create a new data frame for independent variables  
NewData_0b <- expand.grid(Location=unique(aggr.locationb$Location),
                        YEAR=seq((min(aggr.location$YEAR)), (max(aggr.locationb$YEAR))))
pred_0b <- predict(model0b, newdata=NewData_0b, level=0)
#summary(pred_0b) 
#length(pred_0b)
  • Plot model predictions
# Using model data 
  Model0_plotb <- ggplot(aggr.locationb, 
                        aes(x=YEAR, y=Pocillopora, colour=Location)) +
      geom_point(aes(fill=factor(Location)),
                 shape = 21, colour = "black",
                 size = 2, stroke = 0.3, alpha=0.5) +
      
  scale_y_continuous("Pocillopora cover (%)", 
                     breaks = seq(0, 80, by=10), 
                     limits = c(-2, 80))+
  scale_x_continuous("", limits = c(1979, 2019),
                     breaks = seq(1980, 2018, by=2), 
                     expand = c(0.0,0.0))+

  geom_line(data=NewData_0b, 
            aes(y=predict(model0b, level=0, newdata=NewData_0b)), size=2)+
  labs(title="Model 1b prediction")

Model 0b (data) plot vs (predicted values)

 Model0b_All<-grid.arrange(Model_0b_data, Model0_plotb, ncol=2)

Pocillopora model 1 (+ multiple comparisons among years)

This model includes data from Chiriqui

  • Aggregated by location
  • Year is a factor
  • Location as a random factor

Results:

  • Model is significant
  • Better normality
model1_final <- lme(
    Pocillopora ~ -1 + Year_F, random = ~1|Location, data=aggr.location)
    summary(model1_final)
## Linear mixed-effects model fit by REML
##   Data: aggr.location 
##        AIC      BIC    logLik
##   553.5645 617.9682 -245.7823
## 
## Random effects:
##  Formula: ~1 | Location
##         (Intercept) Residual
## StdDev:    10.55603 11.48019
## 
## Fixed effects:  Pocillopora ~ -1 + Year_F 
##               Value Std.Error DF   t-value p-value
## Year_F1980 44.29895 10.210061 57  4.338755  0.0001
## Year_F1983 16.57415  9.188955 57  1.803704  0.0766
## Year_F1984 -6.78593  7.632959 57 -0.889030  0.3777
## Year_F1985 -4.34381  7.439948 57 -0.583849  0.5616
## Year_F1986  1.02520 10.210061 57  0.100411  0.9204
## Year_F1987  1.27457 10.210061 57  0.124834  0.9011
## Year_F1988  2.23030 10.210061 57  0.218442  0.8279
## Year_F1989 -2.07795  9.083723 57 -0.228756  0.8199
## Year_F1990 -0.94790  9.083723 57 -0.104352  0.9173
## Year_F1992  4.16000 10.210061 57  0.407441  0.6852
## Year_F1993  4.83406 10.210061 57  0.473461  0.6377
## Year_F1994  3.94642  9.004154 57  0.438289  0.6628
## Year_F1995 10.16016  9.004154 57  1.128386  0.2639
## Year_F1997 13.98328  7.977199 57  1.752906  0.0850
## Year_F1998 15.45352 10.191919 57  1.516252  0.1350
## Year_F2000 19.65706  9.004154 57  2.183110  0.0332
## Year_F2001 20.71683 10.192208 57  2.032614  0.0468
## Year_F2002 29.00607  9.004154 57  3.221409  0.0021
## Year_F2003 31.38803  9.004154 57  3.485950  0.0010
## Year_F2004 36.30428 10.210061 57  3.555736  0.0008
## Year_F2005 34.95335  9.004154 57  3.881914  0.0003
## Year_F2006 43.60831 10.192208 57  4.278593  0.0001
## Year_F2007 38.34011  9.004154 57  4.258047  0.0001
## Year_F2010 43.32774  9.004154 57  4.811973  0.0000
## Year_F2014 46.40007  9.004154 57  5.153185  0.0000
## Year_F2015 47.75547  9.004154 57  5.303715  0.0000
## Year_F2016 40.01622  9.004154 57  4.444195  0.0000
## Year_F2017 54.79270  9.004154 57  6.085269  0.0000
## Year_F2018 56.34970  9.004154 57  6.258189  0.0000
##  Correlation: 
##            Y_F1980 Y_F1983 Y_F1984 Y_F1985 Y_F1986 Y_F1987 Y_F1988 Y_F1989
## Year_F1983 0.409                                                          
## Year_F1984 0.492   0.525                                                  
## Year_F1985 0.505   0.545   0.689                                          
## Year_F1986 0.368   0.409   0.492   0.505                                  
## Year_F1987 0.368   0.409   0.492   0.505   0.368                          
## Year_F1988 0.368   0.409   0.492   0.505   0.368   0.368                  
## Year_F1989 0.413   0.451   0.560   0.573   0.413   0.413   0.413          
## Year_F1990 0.413   0.451   0.560   0.573   0.413   0.413   0.413   0.468  
## Year_F1992 0.368   0.409   0.492   0.505   0.368   0.368   0.368   0.413  
## Year_F1993 0.368   0.409   0.492   0.505   0.368   0.368   0.368   0.413  
## Year_F1994 0.404   0.449   0.540   0.554   0.404   0.404   0.404   0.454  
## Year_F1995 0.404   0.449   0.540   0.554   0.404   0.404   0.404   0.454  
## Year_F1997 0.453   0.509   0.601   0.618   0.453   0.453   0.453   0.507  
## Year_F1998 0.351   0.402   0.460   0.475   0.351   0.351   0.351   0.391  
## Year_F2000 0.404   0.449   0.540   0.554   0.404   0.404   0.404   0.454  
## Year_F2001 0.351   0.379   0.480   0.489   0.351   0.351   0.351   0.399  
## Year_F2002 0.404   0.449   0.540   0.554   0.404   0.404   0.404   0.454  
## Year_F2003 0.404   0.449   0.540   0.554   0.404   0.404   0.404   0.454  
## Year_F2004 0.368   0.409   0.492   0.505   0.368   0.368   0.368   0.413  
## Year_F2005 0.404   0.449   0.540   0.554   0.404   0.404   0.404   0.454  
## Year_F2006 0.351   0.379   0.480   0.489   0.351   0.351   0.351   0.399  
## Year_F2007 0.404   0.449   0.540   0.554   0.404   0.404   0.404   0.454  
## Year_F2010 0.404   0.449   0.540   0.554   0.404   0.404   0.404   0.454  
## Year_F2014 0.404   0.449   0.540   0.554   0.404   0.404   0.404   0.454  
## Year_F2015 0.404   0.449   0.540   0.554   0.404   0.404   0.404   0.454  
## Year_F2016 0.404   0.449   0.540   0.554   0.404   0.404   0.404   0.454  
## Year_F2017 0.404   0.449   0.540   0.554   0.404   0.404   0.404   0.454  
## Year_F2018 0.404   0.449   0.540   0.554   0.404   0.404   0.404   0.454  
##            Y_F1990 Y_F1992 Y_F1993 Y_F1994 Y_F1995 Y_F1997 Y_F1998 Y_F2000
## Year_F1983                                                                
## Year_F1984                                                                
## Year_F1985                                                                
## Year_F1986                                                                
## Year_F1987                                                                
## Year_F1988                                                                
## Year_F1989                                                                
## Year_F1990                                                                
## Year_F1992 0.413                                                          
## Year_F1993 0.413   0.368                                                  
## Year_F1994 0.454   0.404   0.404                                          
## Year_F1995 0.454   0.404   0.404   0.458                                  
## Year_F1997 0.507   0.453   0.453   0.517   0.517                          
## Year_F1998 0.391   0.351   0.351   0.405   0.405   0.461                  
## Year_F2000 0.454   0.404   0.404   0.458   0.458   0.517   0.405          
## Year_F2001 0.399   0.351   0.351   0.405   0.405   0.456   0.355   0.405  
## Year_F2002 0.454   0.404   0.404   0.458   0.458   0.517   0.405   0.458  
## Year_F2003 0.454   0.404   0.404   0.458   0.458   0.517   0.405   0.458  
## Year_F2004 0.413   0.368   0.368   0.404   0.404   0.453   0.351   0.404  
## Year_F2005 0.454   0.404   0.404   0.458   0.458   0.517   0.405   0.458  
## Year_F2006 0.399   0.351   0.351   0.405   0.405   0.456   0.355   0.405  
## Year_F2007 0.454   0.404   0.404   0.458   0.458   0.517   0.405   0.458  
## Year_F2010 0.454   0.404   0.404   0.458   0.458   0.517   0.405   0.458  
## Year_F2014 0.454   0.404   0.404   0.458   0.458   0.517   0.405   0.458  
## Year_F2015 0.454   0.404   0.404   0.458   0.458   0.517   0.405   0.458  
## Year_F2016 0.454   0.404   0.404   0.458   0.458   0.517   0.405   0.458  
## Year_F2017 0.454   0.404   0.404   0.458   0.458   0.517   0.405   0.458  
## Year_F2018 0.454   0.404   0.404   0.458   0.458   0.517   0.405   0.458  
##            Y_F2001 Y_F2002 Y_F2003 Y_F2004 Y_F2005 Y_F2006 Y_F2007 Y_F2010
## Year_F1983                                                                
## Year_F1984                                                                
## Year_F1985                                                                
## Year_F1986                                                                
## Year_F1987                                                                
## Year_F1988                                                                
## Year_F1989                                                                
## Year_F1990                                                                
## Year_F1992                                                                
## Year_F1993                                                                
## Year_F1994                                                                
## Year_F1995                                                                
## Year_F1997                                                                
## Year_F1998                                                                
## Year_F2000                                                                
## Year_F2001                                                                
## Year_F2002 0.405                                                          
## Year_F2003 0.405   0.458                                                  
## Year_F2004 0.351   0.404   0.404                                          
## Year_F2005 0.405   0.458   0.458   0.404                                  
## Year_F2006 0.366   0.405   0.405   0.351   0.405                          
## Year_F2007 0.405   0.458   0.458   0.404   0.458   0.405                  
## Year_F2010 0.405   0.458   0.458   0.404   0.458   0.405   0.458          
## Year_F2014 0.405   0.458   0.458   0.404   0.458   0.405   0.458   0.458  
## Year_F2015 0.405   0.458   0.458   0.404   0.458   0.405   0.458   0.458  
## Year_F2016 0.405   0.458   0.458   0.404   0.458   0.405   0.458   0.458  
## Year_F2017 0.405   0.458   0.458   0.404   0.458   0.405   0.458   0.458  
## Year_F2018 0.405   0.458   0.458   0.404   0.458   0.405   0.458   0.458  
##            Y_F2014 Y_F2015 Y_F2016 Y_F2017
## Year_F1983                                
## Year_F1984                                
## Year_F1985                                
## Year_F1986                                
## Year_F1987                                
## Year_F1988                                
## Year_F1989                                
## Year_F1990                                
## Year_F1992                                
## Year_F1993                                
## Year_F1994                                
## Year_F1995                                
## Year_F1997                                
## Year_F1998                                
## Year_F2000                                
## Year_F2001                                
## Year_F2002                                
## Year_F2003                                
## Year_F2004                                
## Year_F2005                                
## Year_F2006                                
## Year_F2007                                
## Year_F2010                                
## Year_F2014                                
## Year_F2015 0.458                          
## Year_F2016 0.458   0.458                  
## Year_F2017 0.458   0.458   0.458          
## Year_F2018 0.458   0.458   0.458   0.458  
## 
## Standardized Within-Group Residuals:
##        Min         Q1        Med         Q3        Max 
## -1.9719022 -0.5347533 -0.1131969  0.6440439  1.9719022 
## 
## Number of Observations: 88
## Number of Groups: 3
    anova(model1_final)
  plot(ranef(model1_final))    # Symmetrical scatter effects around zero?
  plot(model1_final)           # plot residuals vs fitted
  resnorm1 <- resid(model1_final)
  hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
  coef.m1 <- as.data.frame(coef(summary(model1_final)))    # Coefficients of the model
  
  plot(model1_final, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
  plot(model1_final, Pocillopora ~ fitted(.), abline = c(0,1))

# Multicomp emmeans
    Year_F.emm<-emmeans(model1_final, ~Year_F)
    #contrast(Year_F.emm, "tukey")
    year_groups<-cld(Year_F.emm, by=NULL) # compact-letter display
    year_groups<-year_groups[order(year_groups$Year_F),] 
    year_groups
    write.csv(year_groups, "Outputs/UvaPocilloTukey.csv", row.names = F)

Multiple comparisons among years

  • Too many lines!

Summary:

  • 1980 is different from 1983-2001) -> Coral cover lose after 1981-82 ENSO
  • “Recovery” by ~2002 (no differences between 1980 and 2002) uninterrupted until 2018 -> no significant cover loss in 1997-98 nor 2015-16
# Multicomp emmeans glht
  m.comp_Pocillopora <- glht(model1_final, linfct = mcp(Year_F = "Tukey"))
  Model1_multipcomp<-summary(m.comp_Pocillopora, test = univariate())
  Model1_multipcomp
## 
##   Simultaneous Tests for General Linear Hypotheses
## 
## Multiple Comparisons of Means: Tukey Contrasts
## 
## 
## Fit: lme.formula(fixed = Pocillopora ~ -1 + Year_F, data = aggr.location, 
##     random = ~1 | Location)
## 
## Linear Hypotheses:
##                  Estimate Std. Error z value Pr(>|z|)    
## 1983 - 1980 == 0 -27.7248    10.5818  -2.620 0.008792 ** 
## 1984 - 1980 == 0 -51.0849     9.2639  -5.514 3.50e-08 ***
## 1985 - 1980 == 0 -48.6428     9.1054  -5.342 9.18e-08 ***
## 1986 - 1980 == 0 -43.2738    11.4802  -3.769 0.000164 ***
## 1987 - 1980 == 0 -43.0244    11.4802  -3.748 0.000178 ***
## 1988 - 1980 == 0 -42.0687    11.4802  -3.664 0.000248 ***
## 1989 - 1980 == 0 -46.3769    10.4913  -4.421 9.85e-06 ***
## 1990 - 1980 == 0 -45.2469    10.4913  -4.313 1.61e-05 ***
## 1992 - 1980 == 0 -40.1390    11.4802  -3.496 0.000472 ***
## 1993 - 1980 == 0 -39.4649    11.4802  -3.438 0.000587 ***
## 1994 - 1980 == 0 -40.3525    10.5373  -3.830 0.000128 ***
## 1995 - 1980 == 0 -34.1388    10.5373  -3.240 0.001196 ** 
## 1997 - 1980 == 0 -30.3157     9.6992  -3.126 0.001774 ** 
## 1998 - 1980 == 0 -28.8454    11.6204  -2.482 0.013053 *  
## 2000 - 1980 == 0 -24.6419    10.5373  -2.339 0.019359 *  
## 2001 - 1980 == 0 -23.5821    11.6211  -2.029 0.042433 *  
## 2002 - 1980 == 0 -15.2929    10.5373  -1.451 0.146692    
## 2003 - 1980 == 0 -12.9109    10.5373  -1.225 0.220476    
## 2004 - 1980 == 0  -7.9947    11.4802  -0.696 0.486185    
## 2005 - 1980 == 0  -9.3456    10.5373  -0.887 0.375127    
## 2006 - 1980 == 0  -0.6906    11.6211  -0.059 0.952610    
## 2007 - 1980 == 0  -5.9588    10.5373  -0.566 0.571732    
## 2010 - 1980 == 0  -0.9712    10.5373  -0.092 0.926564    
## 2014 - 1980 == 0   2.1011    10.5373   0.199 0.841950    
## 2015 - 1980 == 0   3.4565    10.5373   0.328 0.742891    
## 2016 - 1980 == 0  -4.2827    10.5373  -0.406 0.684421    
## 2017 - 1980 == 0  10.4938    10.5373   0.996 0.319313    
## 2018 - 1980 == 0  12.0507    10.5373   1.144 0.252776    
## 1984 - 1983 == 0 -23.3601     8.3105  -2.811 0.004940 ** 
## 1985 - 1983 == 0 -20.9180     8.0767  -2.590 0.009600 ** 
## 1986 - 1983 == 0 -15.5490    10.5818  -1.469 0.141723    
## 1987 - 1983 == 0 -15.2996    10.5818  -1.446 0.148222    
## 1988 - 1983 == 0 -14.3439    10.5818  -1.356 0.175252    
## 1989 - 1983 == 0 -18.6521     9.5748  -1.948 0.051411 .  
## 1990 - 1983 == 0 -17.5221     9.5748  -1.830 0.067248 .  
## 1992 - 1983 == 0 -12.4142    10.5818  -1.173 0.240731    
## 1993 - 1983 == 0 -11.7401    10.5818  -1.109 0.267232    
## 1994 - 1983 == 0 -12.6277     9.5512  -1.322 0.186131    
## 1995 - 1983 == 0  -6.4140     9.5512  -0.672 0.501877    
## 1997 - 1983 == 0  -2.5909     8.5680  -0.302 0.762354    
## 1998 - 1983 == 0  -1.1206    10.6341  -0.105 0.916073    
## 2000 - 1983 == 0   3.0829     9.5512   0.323 0.746864    
## 2001 - 1983 == 0   4.1427    10.8348   0.382 0.702204    
## 2002 - 1983 == 0  12.4319     9.5512   1.302 0.193050    
## 2003 - 1983 == 0  14.8139     9.5512   1.551 0.120902    
## 2004 - 1983 == 0  19.7301    10.5818   1.865 0.062247 .  
## 2005 - 1983 == 0  18.3792     9.5512   1.924 0.054319 .  
## 2006 - 1983 == 0  27.0342    10.8348   2.495 0.012592 *  
## 2007 - 1983 == 0  21.7660     9.5512   2.279 0.022675 *  
## 2010 - 1983 == 0  26.7536     9.5512   2.801 0.005093 ** 
## 2014 - 1983 == 0  29.8259     9.5512   3.123 0.001792 ** 
## 2015 - 1983 == 0  31.1813     9.5512   3.265 0.001096 ** 
## 2016 - 1983 == 0  23.4421     9.5512   2.454 0.014114 *  
## 2017 - 1983 == 0  38.2185     9.5512   4.001 6.30e-05 ***
## 2018 - 1983 == 0  39.7755     9.5512   4.164 3.12e-05 ***
## 1985 - 1984 == 0   2.4421     5.9498   0.410 0.681475    
## 1986 - 1984 == 0   7.8111     9.2639   0.843 0.399128    
## 1987 - 1984 == 0   8.0605     9.2639   0.870 0.384247    
## 1988 - 1984 == 0   9.0162     9.2639   0.973 0.330421    
## 1989 - 1984 == 0   4.7080     7.9417   0.593 0.553304    
## 1990 - 1984 == 0   5.8380     7.9417   0.735 0.462273    
## 1992 - 1984 == 0  10.9459     9.2639   1.182 0.237377    
## 1993 - 1984 == 0  11.6200     9.2639   1.254 0.209722    
## 1994 - 1984 == 0  10.7324     8.0654   1.331 0.183298    
## 1995 - 1984 == 0  16.9461     8.0654   2.101 0.035633 *  
## 1997 - 1984 == 0  20.7692     6.9787   2.976 0.002920 ** 
## 1998 - 1984 == 0  22.2394     9.5173   2.337 0.019452 *  
## 2000 - 1984 == 0  26.4430     8.0654   3.279 0.001043 ** 
## 2001 - 1984 == 0  27.5028     9.3558   2.940 0.003286 ** 
## 2002 - 1984 == 0  35.7920     8.0654   4.438 9.09e-06 ***
## 2003 - 1984 == 0  38.1740     8.0654   4.733 2.21e-06 ***
## 2004 - 1984 == 0  43.0902     9.2639   4.651 3.30e-06 ***
## 2005 - 1984 == 0  41.7393     8.0654   5.175 2.28e-07 ***
## 2006 - 1984 == 0  50.3942     9.3558   5.386 7.19e-08 ***
## 2007 - 1984 == 0  45.1260     8.0654   5.595 2.21e-08 ***
## 2010 - 1984 == 0  50.1137     8.0654   6.213 5.18e-10 ***
## 2014 - 1984 == 0  53.1860     8.0654   6.594 4.27e-11 ***
## 2015 - 1984 == 0  54.5414     8.0654   6.762 1.36e-11 ***
## 2016 - 1984 == 0  46.8021     8.0654   5.803 6.52e-09 ***
## 2017 - 1984 == 0  61.5786     8.0654   7.635 2.26e-14 ***
## 2018 - 1984 == 0  63.1356     8.0654   7.828 4.88e-15 ***
## 1986 - 1985 == 0   5.3690     9.1054   0.590 0.555424    
## 1987 - 1985 == 0   5.6184     9.1054   0.617 0.537209    
## 1988 - 1985 == 0   6.5741     9.1054   0.722 0.470293    
## 1989 - 1985 == 0   2.2659     7.7760   0.291 0.770751    
## 1990 - 1985 == 0   3.3959     7.7760   0.437 0.662316    
## 1992 - 1985 == 0   8.5038     9.1054   0.934 0.350339    
## 1993 - 1985 == 0   9.1779     9.1054   1.008 0.313473    
## 1994 - 1985 == 0   8.2902     7.8830   1.052 0.292954    
## 1995 - 1985 == 0  14.5040     7.8830   1.840 0.065781 .  
## 1997 - 1985 == 0  18.3271     6.7535   2.714 0.006653 ** 
## 1998 - 1985 == 0  19.7973     9.3386   2.120 0.034012 *  
## 2000 - 1985 == 0  24.0009     7.8830   3.045 0.002330 ** 
## 2001 - 1985 == 0  25.0606     9.2240   2.717 0.006590 ** 
## 2002 - 1985 == 0  33.3499     7.8830   4.231 2.33e-05 ***
## 2003 - 1985 == 0  35.7318     7.8830   4.533 5.82e-06 ***
## 2004 - 1985 == 0  40.6481     9.1054   4.464 8.04e-06 ***
## 2005 - 1985 == 0  39.2972     7.8830   4.985 6.19e-07 ***
## 2006 - 1985 == 0  47.9521     9.2240   5.199 2.01e-07 ***
## 2007 - 1985 == 0  42.6839     7.8830   5.415 6.14e-08 ***
## 2010 - 1985 == 0  47.6716     7.8830   6.047 1.47e-09 ***
## 2014 - 1985 == 0  50.7439     7.8830   6.437 1.22e-10 ***
## 2015 - 1985 == 0  52.0993     7.8830   6.609 3.87e-11 ***
## 2016 - 1985 == 0  44.3600     7.8830   5.627 1.83e-08 ***
## 2017 - 1985 == 0  59.1365     7.8830   7.502 6.28e-14 ***
## 2018 - 1985 == 0  60.6935     7.8830   7.699 1.38e-14 ***
## 1987 - 1986 == 0   0.2494    11.4802   0.022 0.982670    
## 1988 - 1986 == 0   1.2051    11.4802   0.105 0.916398    
## 1989 - 1986 == 0  -3.1032    10.4913  -0.296 0.767395    
## 1990 - 1986 == 0  -1.9731    10.4913  -0.188 0.850822    
## 1992 - 1986 == 0   3.1348    11.4802   0.273 0.784806    
## 1993 - 1986 == 0   3.8089    11.4802   0.332 0.740057    
## 1994 - 1986 == 0   2.9212    10.5373   0.277 0.781605    
## 1995 - 1986 == 0   9.1350    10.5373   0.867 0.385986    
## 1997 - 1986 == 0  12.9581     9.6992   1.336 0.181550    
## 1998 - 1986 == 0  14.4283    11.6204   1.242 0.214369    
## 2000 - 1986 == 0  18.6319    10.5373   1.768 0.077029 .  
## 2001 - 1986 == 0  19.6916    11.6211   1.694 0.090176 .  
## 2002 - 1986 == 0  27.9809    10.5373   2.655 0.007921 ** 
## 2003 - 1986 == 0  30.3628    10.5373   2.881 0.003958 ** 
## 2004 - 1986 == 0  35.2791    11.4802   3.073 0.002119 ** 
## 2005 - 1986 == 0  33.9282    10.5373   3.220 0.001283 ** 
## 2006 - 1986 == 0  42.5831    11.6211   3.664 0.000248 ***
## 2007 - 1986 == 0  37.3149    10.5373   3.541 0.000398 ***
## 2010 - 1986 == 0  42.3025    10.5373   4.015 5.96e-05 ***
## 2014 - 1986 == 0  45.3749    10.5373   4.306 1.66e-05 ***
## 2015 - 1986 == 0  46.7303    10.5373   4.435 9.22e-06 ***
## 2016 - 1986 == 0  38.9910    10.5373   3.700 0.000215 ***
## 2017 - 1986 == 0  53.7675    10.5373   5.103 3.35e-07 ***
## 2018 - 1986 == 0  55.3245    10.5373   5.250 1.52e-07 ***
## 1988 - 1987 == 0   0.9557    11.4802   0.083 0.933652    
## 1989 - 1987 == 0  -3.3525    10.4913  -0.320 0.749308    
## 1990 - 1987 == 0  -2.2225    10.4913  -0.212 0.832232    
## 1992 - 1987 == 0   2.8854    11.4802   0.251 0.801551    
## 1993 - 1987 == 0   3.5595    11.4802   0.310 0.756519    
## 1994 - 1987 == 0   2.6719    10.5373   0.254 0.799833    
## 1995 - 1987 == 0   8.8856    10.5373   0.843 0.399086    
## 1997 - 1987 == 0  12.7087     9.6992   1.310 0.190099    
## 1998 - 1987 == 0  14.1790    11.6204   1.220 0.222396    
## 2000 - 1987 == 0  18.3825    10.5373   1.745 0.081068 .  
## 2001 - 1987 == 0  19.4423    11.6211   1.673 0.094325 .  
## 2002 - 1987 == 0  27.7315    10.5373   2.632 0.008494 ** 
## 2003 - 1987 == 0  30.1135    10.5373   2.858 0.004266 ** 
## 2004 - 1987 == 0  35.0297    11.4802   3.051 0.002278 ** 
## 2005 - 1987 == 0  33.6788    10.5373   3.196 0.001393 ** 
## 2006 - 1987 == 0  42.3337    11.6211   3.643 0.000270 ***
## 2007 - 1987 == 0  37.0655    10.5373   3.518 0.000436 ***
## 2010 - 1987 == 0  42.0532    10.5373   3.991 6.58e-05 ***
## 2014 - 1987 == 0  45.1255    10.5373   4.282 1.85e-05 ***
## 2015 - 1987 == 0  46.4809    10.5373   4.411 1.03e-05 ***
## 2016 - 1987 == 0  38.7417    10.5373   3.677 0.000236 ***
## 2017 - 1987 == 0  53.5181    10.5373   5.079 3.80e-07 ***
## 2018 - 1987 == 0  55.0751    10.5373   5.227 1.73e-07 ***
## 1989 - 1988 == 0  -4.3083    10.4913  -0.411 0.681329    
## 1990 - 1988 == 0  -3.1782    10.4913  -0.303 0.761937    
## 1992 - 1988 == 0   1.9297    11.4802   0.168 0.866513    
## 1993 - 1988 == 0   2.6038    11.4802   0.227 0.820576    
## 1994 - 1988 == 0   1.7161    10.5373   0.163 0.870627    
## 1995 - 1988 == 0   7.9299    10.5373   0.753 0.451718    
## 1997 - 1988 == 0  11.7530     9.6992   1.212 0.225608    
## 1998 - 1988 == 0  13.2232    11.6204   1.138 0.255148    
## 2000 - 1988 == 0  17.4268    10.5373   1.654 0.098163 .  
## 2001 - 1988 == 0  18.4865    11.6211   1.591 0.111662    
## 2002 - 1988 == 0  26.7758    10.5373   2.541 0.011052 *  
## 2003 - 1988 == 0  29.1577    10.5373   2.767 0.005656 ** 
## 2004 - 1988 == 0  34.0740    11.4802   2.968 0.002997 ** 
## 2005 - 1988 == 0  32.7230    10.5373   3.105 0.001900 ** 
## 2006 - 1988 == 0  41.3780    11.6211   3.561 0.000370 ***
## 2007 - 1988 == 0  36.1098    10.5373   3.427 0.000611 ***
## 2010 - 1988 == 0  41.0974    10.5373   3.900 9.61e-05 ***
## 2014 - 1988 == 0  44.1698    10.5373   4.192 2.77e-05 ***
## 2015 - 1988 == 0  45.5252    10.5373   4.320 1.56e-05 ***
## 2016 - 1988 == 0  37.7859    10.5373   3.586 0.000336 ***
## 2017 - 1988 == 0  52.5624    10.5373   4.988 6.09e-07 ***
## 2018 - 1988 == 0  54.1194    10.5373   5.136 2.81e-07 ***
## 1990 - 1989 == 0   1.1301     9.3735   0.121 0.904041    
## 1992 - 1989 == 0   6.2380    10.4913   0.595 0.552122    
## 1993 - 1989 == 0   6.9120    10.4913   0.659 0.510003    
## 1994 - 1989 == 0   6.0244     9.4500   0.638 0.523799    
## 1995 - 1989 == 0  12.2381     9.4500   1.295 0.195307    
## 1997 - 1989 == 0  16.0612     8.5222   1.885 0.059480 .  
## 1998 - 1989 == 0  17.5315    10.6778   1.642 0.100618    
## 2000 - 1989 == 0  21.7350     9.4500   2.300 0.021448 *  
## 2001 - 1989 == 0  22.7948    10.6114   2.148 0.031703 *  
## 2002 - 1989 == 0  31.0840     9.4500   3.289 0.001004 ** 
## 2003 - 1989 == 0  33.4660     9.4500   3.541 0.000398 ***
## 2004 - 1989 == 0  38.3822    10.4913   3.658 0.000254 ***
## 2005 - 1989 == 0  37.0313     9.4500   3.919 8.90e-05 ***
## 2006 - 1989 == 0  45.6863    10.6114   4.305 1.67e-05 ***
## 2007 - 1989 == 0  40.4181     9.4500   4.277 1.89e-05 ***
## 2010 - 1989 == 0  45.4057     9.4500   4.805 1.55e-06 ***
## 2014 - 1989 == 0  48.4780     9.4500   5.130 2.90e-07 ***
## 2015 - 1989 == 0  49.8334     9.4500   5.273 1.34e-07 ***
## 2016 - 1989 == 0  42.0942     9.4500   4.454 8.41e-06 ***
## 2017 - 1989 == 0  56.8707     9.4500   6.018 1.77e-09 ***
## 2018 - 1989 == 0  58.4277     9.4500   6.183 6.30e-10 ***
## 1992 - 1990 == 0   5.1079    10.4913   0.487 0.626350    
## 1993 - 1990 == 0   5.7820    10.4913   0.551 0.581551    
## 1994 - 1990 == 0   4.8943     9.4500   0.518 0.604515    
## 1995 - 1990 == 0  11.1081     9.4500   1.175 0.239812    
## 1997 - 1990 == 0  14.9312     8.5222   1.752 0.079768 .  
## 1998 - 1990 == 0  16.4014    10.6778   1.536 0.124530    
## 2000 - 1990 == 0  20.6050     9.4500   2.180 0.029226 *  
## 2001 - 1990 == 0  21.6647    10.6114   2.042 0.041187 *  
## 2002 - 1990 == 0  29.9540     9.4500   3.170 0.001526 ** 
## 2003 - 1990 == 0  32.3359     9.4500   3.422 0.000622 ***
## 2004 - 1990 == 0  37.2522    10.4913   3.551 0.000384 ***
## 2005 - 1990 == 0  35.9013     9.4500   3.799 0.000145 ***
## 2006 - 1990 == 0  44.5562    10.6114   4.199 2.68e-05 ***
## 2007 - 1990 == 0  39.2880     9.4500   4.157 3.22e-05 ***
## 2010 - 1990 == 0  44.2756     9.4500   4.685 2.80e-06 ***
## 2014 - 1990 == 0  47.3480     9.4500   5.010 5.43e-07 ***
## 2015 - 1990 == 0  48.7034     9.4500   5.154 2.55e-07 ***
## 2016 - 1990 == 0  40.9641     9.4500   4.335 1.46e-05 ***
## 2017 - 1990 == 0  55.7406     9.4500   5.898 3.67e-09 ***
## 2018 - 1990 == 0  57.2976     9.4500   6.063 1.33e-09 ***
## 1993 - 1992 == 0   0.6741    11.4802   0.059 0.953179    
## 1994 - 1992 == 0  -0.2136    10.5373  -0.020 0.983829    
## 1995 - 1992 == 0   6.0002    10.5373   0.569 0.569069    
## 1997 - 1992 == 0   9.8233     9.6992   1.013 0.311158    
## 1998 - 1992 == 0  11.2935    11.6204   0.972 0.331114    
## 2000 - 1992 == 0  15.4971    10.5373   1.471 0.141374    
## 2001 - 1992 == 0  16.5568    11.6211   1.425 0.154239    
## 2002 - 1992 == 0  24.8461    10.5373   2.358 0.018377 *  
## 2003 - 1992 == 0  27.2280    10.5373   2.584 0.009767 ** 
## 2004 - 1992 == 0  32.1443    11.4802   2.800 0.005111 ** 
## 2005 - 1992 == 0  30.7934    10.5373   2.922 0.003474 ** 
## 2006 - 1992 == 0  39.4483    11.6211   3.395 0.000687 ***
## 2007 - 1992 == 0  34.1801    10.5373   3.244 0.001180 ** 
## 2010 - 1992 == 0  39.1677    10.5373   3.717 0.000202 ***
## 2014 - 1992 == 0  42.2401    10.5373   4.009 6.11e-05 ***
## 2015 - 1992 == 0  43.5955    10.5373   4.137 3.51e-05 ***
## 2016 - 1992 == 0  35.8562    10.5373   3.403 0.000667 ***
## 2017 - 1992 == 0  50.6327    10.5373   4.805 1.55e-06 ***
## 2018 - 1992 == 0  52.1897    10.5373   4.953 7.31e-07 ***
## 1994 - 1993 == 0  -0.8876    10.5373  -0.084 0.932867    
## 1995 - 1993 == 0   5.3261    10.5373   0.505 0.613240    
## 1997 - 1993 == 0   9.1492     9.6992   0.943 0.345529    
## 1998 - 1993 == 0  10.6195    11.6204   0.914 0.360788    
## 2000 - 1993 == 0  14.8230    10.5373   1.407 0.159510    
## 2001 - 1993 == 0  15.8828    11.6211   1.367 0.171715    
## 2002 - 1993 == 0  24.1720    10.5373   2.294 0.021793 *  
## 2003 - 1993 == 0  26.5540    10.5373   2.520 0.011735 *  
## 2004 - 1993 == 0  31.4702    11.4802   2.741 0.006120 ** 
## 2005 - 1993 == 0  30.1193    10.5373   2.858 0.004258 ** 
## 2006 - 1993 == 0  38.7742    11.6211   3.337 0.000848 ***
## 2007 - 1993 == 0  33.5060    10.5373   3.180 0.001474 ** 
## 2010 - 1993 == 0  38.4937    10.5373   3.653 0.000259 ***
## 2014 - 1993 == 0  41.5660    10.5373   3.945 7.99e-05 ***
## 2015 - 1993 == 0  42.9214    10.5373   4.073 4.64e-05 ***
## 2016 - 1993 == 0  35.1822    10.5373   3.339 0.000841 ***
## 2017 - 1993 == 0  49.9586    10.5373   4.741 2.13e-06 ***
## 2018 - 1993 == 0  51.5156    10.5373   4.889 1.01e-06 ***
## 1995 - 1994 == 0   6.2137     9.3735   0.663 0.507393    
## 1997 - 1994 == 0  10.0369     8.3919   1.196 0.231690    
## 1998 - 1994 == 0  11.5071    10.5197   1.094 0.274015    
## 2000 - 1994 == 0  15.7106     9.3735   1.676 0.093726 .  
## 2001 - 1994 == 0  16.7704    10.5200   1.594 0.110902    
## 2002 - 1994 == 0  25.0596     9.3735   2.673 0.007508 ** 
## 2003 - 1994 == 0  27.4416     9.3735   2.928 0.003416 ** 
## 2004 - 1994 == 0  32.3579    10.5373   3.071 0.002135 ** 
## 2005 - 1994 == 0  31.0069     9.3735   3.308 0.000940 ***
## 2006 - 1994 == 0  39.6619    10.5200   3.770 0.000163 ***
## 2007 - 1994 == 0  34.3937     9.3735   3.669 0.000243 ***
## 2010 - 1994 == 0  39.3813     9.3735   4.201 2.65e-05 ***
## 2014 - 1994 == 0  42.4537     9.3735   4.529 5.92e-06 ***
## 2015 - 1994 == 0  43.8090     9.3735   4.674 2.96e-06 ***
## 2016 - 1994 == 0  36.0698     9.3735   3.848 0.000119 ***
## 2017 - 1994 == 0  50.8463     9.3735   5.424 5.81e-08 ***
## 2018 - 1994 == 0  52.4033     9.3735   5.591 2.26e-08 ***
## 1997 - 1995 == 0   3.8231     8.3919   0.456 0.648698    
## 1998 - 1995 == 0   5.2934    10.5197   0.503 0.614833    
## 2000 - 1995 == 0   9.4969     9.3735   1.013 0.310983    
## 2001 - 1995 == 0  10.5567    10.5200   1.003 0.315625    
## 2002 - 1995 == 0  18.8459     9.3735   2.011 0.044374 *  
## 2003 - 1995 == 0  21.2279     9.3735   2.265 0.023534 *  
## 2004 - 1995 == 0  26.1441    10.5373   2.481 0.013097 *  
## 2005 - 1995 == 0  24.7932     9.3735   2.645 0.008169 ** 
## 2006 - 1995 == 0  33.4482    10.5200   3.179 0.001475 ** 
## 2007 - 1995 == 0  28.1800     9.3735   3.006 0.002644 ** 
## 2010 - 1995 == 0  33.1676     9.3735   3.538 0.000403 ***
## 2014 - 1995 == 0  36.2399     9.3735   3.866 0.000111 ***
## 2015 - 1995 == 0  37.5953     9.3735   4.011 6.05e-05 ***
## 2016 - 1995 == 0  29.8561     9.3735   3.185 0.001447 ** 
## 2017 - 1995 == 0  44.6325     9.3735   4.762 1.92e-06 ***
## 2018 - 1995 == 0  46.1895     9.3735   4.928 8.32e-07 ***
## 1998 - 1997 == 0   1.4702     9.6206   0.153 0.878539    
## 2000 - 1997 == 0   5.6738     8.3919   0.676 0.498976    
## 2001 - 1997 == 0   6.7335     9.6653   0.697 0.486009    
## 2002 - 1997 == 0  15.0228     8.3919   1.790 0.073429 .  
## 2003 - 1997 == 0  17.4048     8.3919   2.074 0.038080 *  
## 2004 - 1997 == 0  22.3210     9.6992   2.301 0.021373 *  
## 2005 - 1997 == 0  20.9701     8.3919   2.499 0.012460 *  
## 2006 - 1997 == 0  29.6250     9.6653   3.065 0.002176 ** 
## 2007 - 1997 == 0  24.3568     8.3919   2.902 0.003703 ** 
## 2010 - 1997 == 0  29.3445     8.3919   3.497 0.000471 ***
## 2014 - 1997 == 0  32.4168     8.3919   3.863 0.000112 ***
## 2015 - 1997 == 0  33.7722     8.3919   4.024 5.71e-05 ***
## 2016 - 1997 == 0  26.0329     8.3919   3.102 0.001921 ** 
## 2017 - 1997 == 0  40.8094     8.3919   4.863 1.16e-06 ***
## 2018 - 1997 == 0  42.3664     8.3919   5.048 4.45e-07 ***
## 2000 - 1998 == 0   4.2035    10.5197   0.400 0.689460    
## 2001 - 1998 == 0   5.2633    11.5733   0.455 0.649266    
## 2002 - 1998 == 0  13.5526    10.5197   1.288 0.197640    
## 2003 - 1998 == 0  15.9345    10.5197   1.515 0.129840    
## 2004 - 1998 == 0  20.8508    11.6204   1.794 0.072761 .  
## 2005 - 1998 == 0  19.4998    10.5197   1.854 0.063789 .  
## 2006 - 1998 == 0  28.1548    11.5733   2.433 0.014985 *  
## 2007 - 1998 == 0  22.8866    10.5197   2.176 0.029585 *  
## 2010 - 1998 == 0  27.8742    10.5197   2.650 0.008056 ** 
## 2014 - 1998 == 0  30.9466    10.5197   2.942 0.003263 ** 
## 2015 - 1998 == 0  32.3019    10.5197   3.071 0.002136 ** 
## 2016 - 1998 == 0  24.5627    10.5197   2.335 0.019547 *  
## 2017 - 1998 == 0  39.3392    10.5197   3.740 0.000184 ***
## 2018 - 1998 == 0  40.8962    10.5197   3.888 0.000101 ***
## 2001 - 2000 == 0   1.0598    10.5200   0.101 0.919758    
## 2002 - 2000 == 0   9.3490     9.3735   0.997 0.318578    
## 2003 - 2000 == 0  11.7310     9.3735   1.251 0.210752    
## 2004 - 2000 == 0  16.6472    10.5373   1.580 0.114142    
## 2005 - 2000 == 0  15.2963     9.3735   1.632 0.102709    
## 2006 - 2000 == 0  23.9513    10.5200   2.277 0.022801 *  
## 2007 - 2000 == 0  18.6831     9.3735   1.993 0.046243 *  
## 2010 - 2000 == 0  23.6707     9.3735   2.525 0.011561 *  
## 2014 - 2000 == 0  26.7430     9.3735   2.853 0.004330 ** 
## 2015 - 2000 == 0  28.0984     9.3735   2.998 0.002721 ** 
## 2016 - 2000 == 0  20.3592     9.3735   2.172 0.029857 *  
## 2017 - 2000 == 0  35.1356     9.3735   3.748 0.000178 ***
## 2018 - 2000 == 0  36.6926     9.3735   3.914 9.06e-05 ***
## 2002 - 2001 == 0   8.2892    10.5200   0.788 0.430724    
## 2003 - 2001 == 0  10.6712    10.5200   1.014 0.310403    
## 2004 - 2001 == 0  15.5875    11.6211   1.341 0.179822    
## 2005 - 2001 == 0  14.2365    10.5200   1.353 0.175964    
## 2006 - 2001 == 0  22.8915    11.4802   1.994 0.046152 *  
## 2007 - 2001 == 0  17.6233    10.5200   1.675 0.093890 .  
## 2010 - 2001 == 0  22.6109    10.5200   2.149 0.031608 *  
## 2014 - 2001 == 0  25.6832    10.5200   2.441 0.014631 *  
## 2015 - 2001 == 0  27.0386    10.5200   2.570 0.010163 *  
## 2016 - 2001 == 0  19.2994    10.5200   1.835 0.066572 .  
## 2017 - 2001 == 0  34.0759    10.5200   3.239 0.001199 ** 
## 2018 - 2001 == 0  35.6329    10.5200   3.387 0.000706 ***
## 2003 - 2002 == 0   2.3820     9.3735   0.254 0.799406    
## 2004 - 2002 == 0   7.2982    10.5373   0.693 0.488554    
## 2005 - 2002 == 0   5.9473     9.3735   0.634 0.525770    
## 2006 - 2002 == 0  14.6022    10.5200   1.388 0.165121    
## 2007 - 2002 == 0   9.3340     9.3735   0.996 0.319354    
## 2010 - 2002 == 0  14.3217     9.3735   1.528 0.126541    
## 2014 - 2002 == 0  17.3940     9.3735   1.856 0.063503 .  
## 2015 - 2002 == 0  18.7494     9.3735   2.000 0.045473 *  
## 2016 - 2002 == 0  11.0102     9.3735   1.175 0.240155    
## 2017 - 2002 == 0  25.7866     9.3735   2.751 0.005941 ** 
## 2018 - 2002 == 0  27.3436     9.3735   2.917 0.003533 ** 
## 2004 - 2003 == 0   4.9162    10.5373   0.467 0.640816    
## 2005 - 2003 == 0   3.5653     9.3735   0.380 0.703678    
## 2006 - 2003 == 0  12.2203    10.5200   1.162 0.245386    
## 2007 - 2003 == 0   6.9521     9.3735   0.742 0.458287    
## 2010 - 2003 == 0  11.9397     9.3735   1.274 0.202745    
## 2014 - 2003 == 0  15.0120     9.3735   1.602 0.109259    
## 2015 - 2003 == 0  16.3674     9.3735   1.746 0.080788 .  
## 2016 - 2003 == 0   8.6282     9.3735   0.920 0.357320    
## 2017 - 2003 == 0  23.4047     9.3735   2.497 0.012529 *  
## 2018 - 2003 == 0  24.9617     9.3735   2.663 0.007745 ** 
## 2005 - 2004 == 0  -1.3509    10.5373  -0.128 0.897987    
## 2006 - 2004 == 0   7.3040    11.6211   0.629 0.529668    
## 2007 - 2004 == 0   2.0358    10.5373   0.193 0.846800    
## 2010 - 2004 == 0   7.0235    10.5373   0.667 0.505068    
## 2014 - 2004 == 0  10.0958    10.5373   0.958 0.338010    
## 2015 - 2004 == 0  11.4512    10.5373   1.087 0.277155    
## 2016 - 2004 == 0   3.7119    10.5373   0.352 0.724637    
## 2017 - 2004 == 0  18.4884    10.5373   1.755 0.079332 .  
## 2018 - 2004 == 0  20.0454    10.5373   1.902 0.057127 .  
## 2006 - 2005 == 0   8.6550    10.5200   0.823 0.410668    
## 2007 - 2005 == 0   3.3868     9.3735   0.361 0.717867    
## 2010 - 2005 == 0   8.3744     9.3735   0.893 0.371639    
## 2014 - 2005 == 0  11.4467     9.3735   1.221 0.222020    
## 2015 - 2005 == 0  12.8021     9.3735   1.366 0.172010    
## 2016 - 2005 == 0   5.0629     9.3735   0.540 0.589112    
## 2017 - 2005 == 0  19.8394     9.3735   2.117 0.034300 *  
## 2018 - 2005 == 0  21.3963     9.3735   2.283 0.022452 *  
## 2007 - 2006 == 0  -5.2682    10.5200  -0.501 0.616525    
## 2010 - 2006 == 0  -0.2806    10.5200  -0.027 0.978723    
## 2014 - 2006 == 0   2.7918    10.5200   0.265 0.790718    
## 2015 - 2006 == 0   4.1472    10.5200   0.394 0.693420    
## 2016 - 2006 == 0  -3.5921    10.5200  -0.341 0.732761    
## 2017 - 2006 == 0  11.1844    10.5200   1.063 0.287710    
## 2018 - 2006 == 0  12.7414    10.5200   1.211 0.225833    
## 2010 - 2007 == 0   4.9876     9.3735   0.532 0.594659    
## 2014 - 2007 == 0   8.0600     9.3735   0.860 0.389864    
## 2015 - 2007 == 0   9.4154     9.3735   1.004 0.315156    
## 2016 - 2007 == 0   1.6761     9.3735   0.179 0.858085    
## 2017 - 2007 == 0  16.4526     9.3735   1.755 0.079222 .  
## 2018 - 2007 == 0  18.0096     9.3735   1.921 0.054691 .  
## 2014 - 2010 == 0   3.0723     9.3735   0.328 0.743088    
## 2015 - 2010 == 0   4.4277     9.3735   0.472 0.636667    
## 2016 - 2010 == 0  -3.3115     9.3735  -0.353 0.723875    
## 2017 - 2010 == 0  11.4650     9.3735   1.223 0.221284    
## 2018 - 2010 == 0  13.0220     9.3735   1.389 0.164764    
## 2015 - 2014 == 0   1.3554     9.3735   0.145 0.885028    
## 2016 - 2014 == 0  -6.3839     9.3735  -0.681 0.495839    
## 2017 - 2014 == 0   8.3926     9.3735   0.895 0.370598    
## 2018 - 2014 == 0   9.9496     9.3735   1.061 0.288481    
## 2016 - 2015 == 0  -7.7392     9.3735  -0.826 0.409003    
## 2017 - 2015 == 0   7.0372     9.3735   0.751 0.452799    
## 2018 - 2015 == 0   8.5942     9.3735   0.917 0.359215    
## 2017 - 2016 == 0  14.7765     9.3735   1.576 0.114933    
## 2018 - 2016 == 0  16.3335     9.3735   1.743 0.081419 .  
## 2018 - 2017 == 0   1.5570     9.3735   0.166 0.868074    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Univariate p values reported)

Model 1 plot (data)

Model1_data <- ggplot(aggr.location, aes(x=YEAR, y=Pocillopora)) +
  geom_boxplot(aes(group=YEAR), outlier.shape = NA) +
  stat_boxplot(aes(group=YEAR), geom = 'errorbar')+
 geom_point(aes(fill=factor(Location)),
                 shape = 21, colour = "black",
                 size = 2, stroke = 0.8, alpha=0.5) +
  stat_summary(fun=mean, geom="line", colour="gray")+

  scale_y_continuous("Pocillopora spp. cover (%)", limits = c(-2, 80),
                     breaks = seq(-0, 80, by=10),
                     expand = c(0,0))+
  scale_x_continuous("", limits = c(1979, 2019),
                     breaks = seq(1980, 2018, by=2), expand = c(0,0))+

  annotate("rect", xmin = 1983, xmax = 1984, 
           ymin = 0, ymax = 80,  alpha = .2, fill="gray")+
  annotate("rect", xmin = 1997.5, xmax = 1998.5, 
           ymin = 0, ymax = 80,  alpha = .2, fill="gray")+
  annotate("rect", xmin = 2015.5, xmax = 2016.5,
           ymin = 0, ymax = 80,  alpha = .2, fill="gray")+
  #ggtitle("Model 2 data")+
  theme(legend.position = c(0.25, 0.8))
Model1_data

#ggsave(file="Outputs/Fig_1b.svg", plot=Model2_data, width=7, height=4.3)

Model 1 (predicted values)

  • Extract model 2 predicted values
# Option 1

  # Create a new data frame for independent variables  
  NewData_1 <- expand.grid(Location=unique(aggr.location$Location),
                          Year_F=unique(aggr.location$Year_F))
  pred_1 <- predict(model1_final , newdata=NewData_1, re.form= ~(1|Location),
                    level=0)
  #summary(pred_1) 
  #length(pred_1)
  
  Predicted_Pocillopora<-cbind(NewData_1, pred_1)
  #write.csv(Predicted_Pocillopora, "Model2Predictions.c")

# Option 2
  # Effect plot
    Model1_plot<-plot(emmeans(model1_final, ~Year_F), comparisons = TRUE) +
        coord_flip(xlim = NULL, ylim = NULL, expand = TRUE) + theme_bw() +
        theme(axis.text.x = element_text(angle = 90)) + 
        ggtitle("Model 2 preditions")
 Model1_All<-grid.arrange(Model1_data, Model1_plot, ncol=2)

Aggregate data (Massives)

  • Hierarchically aggregate by location
# Aggregate by Location
  aggr.location.mas <- aggregate(Massive ~ YEAR+Month+Location, 
                        FUN=mean,data=cover)
  aggr.location.mas$Year_F<-as.factor(aggr.location.mas$YEAR)

Massives model (3)

This model includes aggregated data from Chiriqui

  • Aggregated by location
  • YEAR is a continuous variable
  • Location as a random factor

Model is NOT significant

# All years 1980_2018 
  Model3 <- lme(
    Massive ~ YEAR, random = ~1|Location, data=aggr.location.mas)
  summary(Model3)
## Linear mixed-effects model fit by REML
##   Data: aggr.location.mas 
##        AIC     BIC    logLik
##   125.6804 135.451 -58.84018
## 
## Random effects:
##  Formula: ~1 | Location
##         (Intercept)  Residual
## StdDev:   0.6919983 0.4241932
## 
## Fixed effects:  Massive ~ YEAR 
##                  Value Std.Error DF     t-value p-value
## (Intercept)  0.7419698  8.531140 83  0.08697193  0.9309
## YEAR        -0.0000404  0.004263 83 -0.00948160  0.9925
##  Correlation: 
##      (Intr)
## YEAR -0.999
## 
## Standardized Within-Group Residuals:
##        Min         Q1        Med         Q3        Max 
## -2.3877523 -0.5247623 -0.2869986  0.2727082  3.6837232 
## 
## Number of Observations: 87
## Number of Groups: 3
  anova(Model3)
  #plot(ranef(Model3))    # Symmetrical scatter effects around zero?
  #plot(Model3)           # plot residuals vs fitted
  #resnorm1 <- resid(Model3)
  #hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
  #coef.m1 <- as.data.frame(coef(summary(Model3)))    # Coefficients of the model
  
  #plot(Model3, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
  #plot(Model3, Massive ~ fitted(.), abline = c(0,1))

Model 3 plot (Massives, non-significant)

Massives model 4 (+ multiple comparisons between years)

This model includes data from Chiriqui * aggregated by location * Year is a factor * location as a random factor

  • Model is significant*
# All years 1980_2018 
  Model4 <- lme(
    Massive ~ -1 + Year_F, random = ~1|Location, data=aggr.location.mas)
  #summary(Model4)
  anova(Model4)
  plot(ranef(Model4))    # Symmetrical scatter effects around zero?
  plot(Model4)           # plot residuals vs fitted
  resnorm1 <- resid(Model4)
  hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
  coef.m1 <- as.data.frame(coef(summary(Model4)))    # Coefficients of the model
  
  plot(Model4, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
  plot(Model4, Massive ~ fitted(.), abline = c(0,1))

  # Multicomp
    Year_F.emm<-emmeans(Model4, ~Year_F)
    #contrast(Year_F.emm, "tukey")
    year_groups<-cld(Year_F.emm, by=NULL) # compact-letter display
    year_groups<-year_groups[order(year_groups$Year_F),] 
    year_groups
    write.csv(year_groups, "Outputs/UvaNonPocilloTukey.csv", row.names = F)

Multiple comparisons among years

Summary:

  • 1980 is different from every year (1983-2018) -> Non-Pocillopora coral cover loss after 1981-82 ENSO has not recovered to pre-1982 values
  • 1994-1997 artifact differences by incorporating Uva1m2?
  • 1997 marginally different from 1998 (p=0.06)
  • 1997 different from 1999-2018 (p<0.05), except 2004-2006 -> Massive coral cover lose after 1997-98 ENSO has not recovered to pre-1997 values
m.comp_Massive <- glht(Model4, linfct = mcp(Year_F = "Tukey"))
summary(m.comp_Massive, test = univariate())
## 
##   Simultaneous Tests for General Linear Hypotheses
## 
## Multiple Comparisons of Means: Tukey Contrasts
## 
## 
## Fit: lme.formula(fixed = Massive ~ -1 + Year_F, data = aggr.location.mas, 
##     random = ~1 | Location)
## 
## Linear Hypotheses:
##                    Estimate Std. Error z value Pr(>|z|)    
## 1983 - 1980 == 0 -1.598e+00  4.149e-01  -3.852 0.000117 ***
## 1984 - 1980 == 0 -1.711e+00  3.926e-01  -4.358 1.31e-05 ***
## 1985 - 1980 == 0 -1.712e+00  3.877e-01  -4.415 1.01e-05 ***
## 1986 - 1980 == 0 -1.685e+00  4.426e-01  -3.806 0.000141 ***
## 1987 - 1980 == 0 -1.614e+00  4.426e-01  -3.647 0.000266 ***
## 1988 - 1980 == 0 -1.651e+00  4.426e-01  -3.731 0.000191 ***
## 1989 - 1980 == 0 -1.689e+00  4.197e-01  -4.024 5.71e-05 ***
## 1990 - 1980 == 0 -1.687e+00  4.197e-01  -4.020 5.81e-05 ***
## 1992 - 1980 == 0 -1.563e+00  4.426e-01  -3.531 0.000414 ***
## 1993 - 1980 == 0 -1.374e+00  4.426e-01  -3.104 0.001911 ** 
## 1994 - 1980 == 0 -1.022e+00  4.191e-01  -2.438 0.014749 *  
## 1995 - 1980 == 0 -7.418e-01  4.191e-01  -1.770 0.076716 .  
## 1997 - 1980 == 0 -8.880e-01  3.977e-01  -2.233 0.025560 *  
## 1998 - 1980 == 0 -1.455e+00  4.439e-01  -3.277 0.001049 ** 
## 2000 - 1980 == 0 -1.441e+00  4.191e-01  -3.438 0.000585 ***
## 2001 - 1980 == 0 -1.501e+00  4.489e-01  -3.344 0.000826 ***
## 2002 - 1980 == 0 -1.402e+00  4.191e-01  -3.344 0.000825 ***
## 2003 - 1980 == 0 -1.416e+00  4.191e-01  -3.378 0.000731 ***
## 2004 - 1980 == 0 -1.104e+00  4.426e-01  -2.495 0.012604 *  
## 2005 - 1980 == 0 -1.394e+00  4.191e-01  -3.326 0.000881 ***
## 2006 - 1980 == 0 -1.257e+00  4.489e-01  -2.800 0.005104 ** 
## 2007 - 1980 == 0 -1.414e+00  4.191e-01  -3.375 0.000739 ***
## 2010 - 1980 == 0 -1.414e+00  4.191e-01  -3.374 0.000741 ***
## 2014 - 1980 == 0 -1.488e+00  4.191e-01  -3.551 0.000383 ***
## 2015 - 1980 == 0 -1.432e+00  4.191e-01  -3.417 0.000633 ***
## 2016 - 1980 == 0 -1.761e+00  4.191e-01  -4.201 2.66e-05 ***
## 2017 - 1980 == 0 -1.574e+00  4.191e-01  -3.756 0.000172 ***
## 2018 - 1980 == 0 -1.651e+00  4.191e-01  -3.940 8.15e-05 ***
## 1984 - 1983 == 0 -1.129e-01  2.609e-01  -0.433 0.665274    
## 1985 - 1983 == 0 -1.134e-01  2.534e-01  -0.448 0.654503    
## 1986 - 1983 == 0 -8.662e-02  3.314e-01  -0.261 0.793807    
## 1987 - 1983 == 0 -1.597e-02  3.314e-01  -0.048 0.961564    
## 1988 - 1983 == 0 -5.316e-02  3.314e-01  -0.160 0.872558    
## 1989 - 1983 == 0 -9.082e-02  3.001e-01  -0.303 0.762169    
## 1990 - 1983 == 0 -8.914e-02  3.001e-01  -0.297 0.766421    
## 1992 - 1983 == 0  3.527e-02  3.314e-01   0.106 0.915237    
## 1993 - 1983 == 0  2.244e-01  3.314e-01   0.677 0.498351    
## 1994 - 1983 == 0  5.762e-01  2.993e-01   1.925 0.054186 .  
## 1995 - 1983 == 0  8.563e-01  2.993e-01   2.861 0.004218 ** 
## 1997 - 1983 == 0  7.102e-01  2.685e-01   2.645 0.008168 ** 
## 1998 - 1983 == 0  1.436e-01  3.331e-01   0.431 0.666360    
## 2000 - 1983 == 0  1.571e-01  2.993e-01   0.525 0.599608    
## 2001 - 1983 == 0  9.711e-02  3.398e-01   0.286 0.775029    
## 2002 - 1983 == 0  1.966e-01  2.993e-01   0.657 0.511322    
## 2003 - 1983 == 0  1.826e-01  2.993e-01   0.610 0.541859    
## 2004 - 1983 == 0  4.939e-01  3.314e-01   1.490 0.136115    
## 2005 - 1983 == 0  2.042e-01  2.993e-01   0.682 0.495008    
## 2006 - 1983 == 0  3.411e-01  3.398e-01   1.004 0.315486    
## 2007 - 1983 == 0  1.839e-01  2.993e-01   0.615 0.538878    
## 2010 - 1983 == 0  1.841e-01  2.993e-01   0.615 0.538415    
## 2014 - 1983 == 0  1.098e-01  2.993e-01   0.367 0.713591    
## 2015 - 1983 == 0  1.661e-01  2.993e-01   0.555 0.578987    
## 2016 - 1983 == 0 -1.625e-01  2.993e-01  -0.543 0.587169    
## 2017 - 1983 == 0  2.388e-02  2.993e-01   0.080 0.936408    
## 2018 - 1983 == 0 -5.308e-02  2.993e-01  -0.177 0.859236    
## 1985 - 1984 == 0 -5.331e-04  1.862e-01  -0.003 0.997716    
## 1986 - 1984 == 0  2.625e-02  2.901e-01   0.090 0.927907    
## 1987 - 1984 == 0  9.690e-02  2.901e-01   0.334 0.738353    
## 1988 - 1984 == 0  5.971e-02  2.901e-01   0.206 0.836927    
## 1989 - 1984 == 0  2.205e-02  2.486e-01   0.089 0.929329    
## 1990 - 1984 == 0  2.372e-02  2.486e-01   0.095 0.923982    
## 1992 - 1984 == 0  1.481e-01  2.901e-01   0.511 0.609565    
## 1993 - 1984 == 0  3.373e-01  2.901e-01   1.163 0.244967    
## 1994 - 1984 == 0  6.891e-01  2.527e-01   2.727 0.006393 ** 
## 1995 - 1984 == 0  9.692e-01  2.527e-01   3.836 0.000125 ***
## 1997 - 1984 == 0  8.230e-01  2.189e-01   3.760 0.000170 ***
## 1998 - 1984 == 0  2.565e-01  2.984e-01   0.859 0.390111    
## 2000 - 1984 == 0  2.700e-01  2.527e-01   1.068 0.285344    
## 2001 - 1984 == 0  2.100e-01  2.931e-01   0.716 0.473698    
## 2002 - 1984 == 0  3.094e-01  2.527e-01   1.225 0.220761    
## 2003 - 1984 == 0  2.954e-01  2.527e-01   1.169 0.242361    
## 2004 - 1984 == 0  6.068e-01  2.901e-01   2.092 0.036449 *  
## 2005 - 1984 == 0  3.171e-01  2.527e-01   1.255 0.209549    
## 2006 - 1984 == 0  4.539e-01  2.931e-01   1.549 0.121413    
## 2007 - 1984 == 0  2.968e-01  2.527e-01   1.174 0.240218    
## 2010 - 1984 == 0  2.970e-01  2.527e-01   1.175 0.239885    
## 2014 - 1984 == 0  2.227e-01  2.527e-01   0.881 0.378128    
## 2015 - 1984 == 0  2.789e-01  2.527e-01   1.104 0.269679    
## 2016 - 1984 == 0 -4.962e-02  2.527e-01  -0.196 0.844318    
## 2017 - 1984 == 0  1.367e-01  2.527e-01   0.541 0.588405    
## 2018 - 1984 == 0  5.979e-02  2.527e-01   0.237 0.812954    
## 1986 - 1985 == 0  2.678e-02  2.851e-01   0.094 0.925155    
## 1987 - 1985 == 0  9.743e-02  2.851e-01   0.342 0.732510    
## 1988 - 1985 == 0  6.024e-02  2.851e-01   0.211 0.832637    
## 1989 - 1985 == 0  2.258e-02  2.434e-01   0.093 0.926077    
## 1990 - 1985 == 0  2.426e-02  2.434e-01   0.100 0.920618    
## 1992 - 1985 == 0  1.487e-01  2.851e-01   0.522 0.601977    
## 1993 - 1985 == 0  3.378e-01  2.851e-01   1.185 0.236014    
## 1994 - 1985 == 0  6.896e-01  2.469e-01   2.793 0.005225 ** 
## 1995 - 1985 == 0  9.697e-01  2.469e-01   3.927 8.59e-05 ***
## 1997 - 1985 == 0  8.236e-01  2.117e-01   3.890 0.000100 ***
## 1998 - 1985 == 0  2.570e-01  2.927e-01   0.878 0.379978    
## 2000 - 1985 == 0  2.705e-01  2.469e-01   1.096 0.273283    
## 2001 - 1985 == 0  2.105e-01  2.889e-01   0.729 0.466269    
## 2002 - 1985 == 0  3.100e-01  2.469e-01   1.255 0.209370    
## 2003 - 1985 == 0  2.960e-01  2.469e-01   1.199 0.230682    
## 2004 - 1985 == 0  6.073e-01  2.851e-01   2.131 0.033122 *  
## 2005 - 1985 == 0  3.176e-01  2.469e-01   1.286 0.198335    
## 2006 - 1985 == 0  4.545e-01  2.889e-01   1.573 0.115751    
## 2007 - 1985 == 0  2.973e-01  2.469e-01   1.204 0.228564    
## 2010 - 1985 == 0  2.975e-01  2.469e-01   1.205 0.228236    
## 2014 - 1985 == 0  2.232e-01  2.469e-01   0.904 0.365931    
## 2015 - 1985 == 0  2.795e-01  2.469e-01   1.132 0.257730    
## 2016 - 1985 == 0 -4.909e-02  2.469e-01  -0.199 0.842414    
## 2017 - 1985 == 0  1.373e-01  2.469e-01   0.556 0.578237    
## 2018 - 1985 == 0  6.032e-02  2.469e-01   0.244 0.806991    
## 1987 - 1986 == 0  7.065e-02  3.593e-01   0.197 0.844127    
## 1988 - 1986 == 0  3.346e-02  3.593e-01   0.093 0.925811    
## 1989 - 1986 == 0 -4.196e-03  3.284e-01  -0.013 0.989805    
## 1990 - 1986 == 0 -2.523e-03  3.284e-01  -0.008 0.993869    
## 1992 - 1986 == 0  1.219e-01  3.593e-01   0.339 0.734436    
## 1993 - 1986 == 0  3.110e-01  3.593e-01   0.866 0.386738    
## 1994 - 1986 == 0  6.628e-01  3.299e-01   2.009 0.044519 *  
## 1995 - 1986 == 0  9.430e-01  3.299e-01   2.858 0.004259 ** 
## 1997 - 1986 == 0  7.968e-01  3.037e-01   2.623 0.008706 ** 
## 1998 - 1986 == 0  2.302e-01  3.639e-01   0.633 0.526983    
## 2000 - 1986 == 0  2.437e-01  3.299e-01   0.739 0.460031    
## 2001 - 1986 == 0  1.837e-01  3.640e-01   0.505 0.613701    
## 2002 - 1986 == 0  2.832e-01  3.299e-01   0.858 0.390686    
## 2003 - 1986 == 0  2.692e-01  3.299e-01   0.816 0.414534    
## 2004 - 1986 == 0  5.806e-01  3.593e-01   1.616 0.106162    
## 2005 - 1986 == 0  2.908e-01  3.299e-01   0.882 0.378002    
## 2006 - 1986 == 0  4.277e-01  3.640e-01   1.175 0.239977    
## 2007 - 1986 == 0  2.705e-01  3.299e-01   0.820 0.412201    
## 2010 - 1986 == 0  2.707e-01  3.299e-01   0.821 0.411838    
## 2014 - 1986 == 0  1.965e-01  3.299e-01   0.596 0.551490    
## 2015 - 1986 == 0  2.527e-01  3.299e-01   0.766 0.443724    
## 2016 - 1986 == 0 -7.587e-02  3.299e-01  -0.230 0.818114    
## 2017 - 1986 == 0  1.105e-01  3.299e-01   0.335 0.737666    
## 2018 - 1986 == 0  3.355e-02  3.299e-01   0.102 0.919007    
## 1988 - 1987 == 0 -3.719e-02  3.593e-01  -0.104 0.917565    
## 1989 - 1987 == 0 -7.485e-02  3.284e-01  -0.228 0.819713    
## 1990 - 1987 == 0 -7.317e-02  3.284e-01  -0.223 0.823676    
## 1992 - 1987 == 0  5.124e-02  3.593e-01   0.143 0.886596    
## 1993 - 1987 == 0  2.404e-01  3.593e-01   0.669 0.503540    
## 1994 - 1987 == 0  5.922e-01  3.299e-01   1.795 0.072651 .  
## 1995 - 1987 == 0  8.723e-01  3.299e-01   2.644 0.008189 ** 
## 1997 - 1987 == 0  7.261e-01  3.037e-01   2.391 0.016813 *  
## 1998 - 1987 == 0  1.596e-01  3.639e-01   0.438 0.661030    
## 2000 - 1987 == 0  1.731e-01  3.299e-01   0.525 0.599834    
## 2001 - 1987 == 0  1.131e-01  3.640e-01   0.311 0.756041    
## 2002 - 1987 == 0  2.125e-01  3.299e-01   0.644 0.519434    
## 2003 - 1987 == 0  1.985e-01  3.299e-01   0.602 0.547318    
## 2004 - 1987 == 0  5.099e-01  3.593e-01   1.419 0.155878    
## 2005 - 1987 == 0  2.202e-01  3.299e-01   0.667 0.504499    
## 2006 - 1987 == 0  3.570e-01  3.640e-01   0.981 0.326627    
## 2007 - 1987 == 0  1.999e-01  3.299e-01   0.606 0.544600    
## 2010 - 1987 == 0  2.001e-01  3.299e-01   0.607 0.544177    
## 2014 - 1987 == 0  1.258e-01  3.299e-01   0.381 0.702926    
## 2015 - 1987 == 0  1.820e-01  3.299e-01   0.552 0.581110    
## 2016 - 1987 == 0 -1.465e-01  3.299e-01  -0.444 0.656951    
## 2017 - 1987 == 0  3.985e-02  3.299e-01   0.121 0.903858    
## 2018 - 1987 == 0 -3.710e-02  3.299e-01  -0.112 0.910450    
## 1989 - 1988 == 0 -3.766e-02  3.284e-01  -0.115 0.908711    
## 1990 - 1988 == 0 -3.598e-02  3.284e-01  -0.110 0.912750    
## 1992 - 1988 == 0  8.844e-02  3.593e-01   0.246 0.805594    
## 1993 - 1988 == 0  2.776e-01  3.593e-01   0.772 0.439859    
## 1994 - 1988 == 0  6.294e-01  3.299e-01   1.908 0.056424 .  
## 1995 - 1988 == 0  9.095e-01  3.299e-01   2.757 0.005835 ** 
## 1997 - 1988 == 0  7.633e-01  3.037e-01   2.513 0.011963 *  
## 1998 - 1988 == 0  1.968e-01  3.639e-01   0.541 0.588727    
## 2000 - 1988 == 0  2.103e-01  3.299e-01   0.637 0.523882    
## 2001 - 1988 == 0  1.503e-01  3.640e-01   0.413 0.679704    
## 2002 - 1988 == 0  2.497e-01  3.299e-01   0.757 0.449079    
## 2003 - 1988 == 0  2.357e-01  3.299e-01   0.715 0.474907    
## 2004 - 1988 == 0  5.471e-01  3.593e-01   1.523 0.127866    
## 2005 - 1988 == 0  2.574e-01  3.299e-01   0.780 0.435296    
## 2006 - 1988 == 0  3.942e-01  3.640e-01   1.083 0.278758    
## 2007 - 1988 == 0  2.371e-01  3.299e-01   0.719 0.472384    
## 2010 - 1988 == 0  2.373e-01  3.299e-01   0.719 0.471992    
## 2014 - 1988 == 0  1.630e-01  3.299e-01   0.494 0.621231    
## 2015 - 1988 == 0  2.192e-01  3.299e-01   0.664 0.506372    
## 2016 - 1988 == 0 -1.093e-01  3.299e-01  -0.331 0.740347    
## 2017 - 1988 == 0  7.704e-02  3.299e-01   0.234 0.815356    
## 2018 - 1988 == 0  8.651e-05  3.299e-01   0.000 0.999791    
## 1990 - 1989 == 0  1.673e-03  2.934e-01   0.006 0.995450    
## 1992 - 1989 == 0  1.261e-01  3.284e-01   0.384 0.701010    
## 1993 - 1989 == 0  3.152e-01  3.284e-01   0.960 0.337133    
## 1994 - 1989 == 0  6.670e-01  2.959e-01   2.254 0.024185 *  
## 1995 - 1989 == 0  9.472e-01  2.959e-01   3.201 0.001370 ** 
## 1997 - 1989 == 0  8.010e-01  2.670e-01   3.000 0.002697 ** 
## 1998 - 1989 == 0  2.344e-01  3.345e-01   0.701 0.483461    
## 2000 - 1989 == 0  2.479e-01  2.959e-01   0.838 0.402111    
## 2001 - 1989 == 0  1.879e-01  3.323e-01   0.565 0.571758    
## 2002 - 1989 == 0  2.874e-01  2.959e-01   0.971 0.331462    
## 2003 - 1989 == 0  2.734e-01  2.959e-01   0.924 0.355557    
## 2004 - 1989 == 0  5.848e-01  3.284e-01   1.781 0.074972 .  
## 2005 - 1989 == 0  2.950e-01  2.959e-01   0.997 0.318741    
## 2006 - 1989 == 0  4.319e-01  3.323e-01   1.299 0.193773    
## 2007 - 1989 == 0  2.747e-01  2.959e-01   0.928 0.353189    
## 2010 - 1989 == 0  2.749e-01  2.959e-01   0.929 0.352821    
## 2014 - 1989 == 0  2.007e-01  2.959e-01   0.678 0.497689    
## 2015 - 1989 == 0  2.569e-01  2.959e-01   0.868 0.385341    
## 2016 - 1989 == 0 -7.167e-02  2.959e-01  -0.242 0.808616    
## 2017 - 1989 == 0  1.147e-01  2.959e-01   0.388 0.698306    
## 2018 - 1989 == 0  3.774e-02  2.959e-01   0.128 0.898506    
## 1992 - 1990 == 0  1.244e-01  3.284e-01   0.379 0.704789    
## 1993 - 1990 == 0  3.135e-01  3.284e-01   0.955 0.339704    
## 1994 - 1990 == 0  6.654e-01  2.959e-01   2.249 0.024542 *  
## 1995 - 1990 == 0  9.455e-01  2.959e-01   3.195 0.001397 ** 
## 1997 - 1990 == 0  7.993e-01  2.670e-01   2.994 0.002753 ** 
## 1998 - 1990 == 0  2.328e-01  3.345e-01   0.696 0.486588    
## 2000 - 1990 == 0  2.463e-01  2.959e-01   0.832 0.405294    
## 2001 - 1990 == 0  1.863e-01  3.323e-01   0.560 0.575186    
## 2002 - 1990 == 0  2.857e-01  2.959e-01   0.966 0.334284    
## 2003 - 1990 == 0  2.717e-01  2.959e-01   0.918 0.358509    
## 2004 - 1990 == 0  5.831e-01  3.284e-01   1.776 0.075809 .  
## 2005 - 1990 == 0  2.934e-01  2.959e-01   0.991 0.321493    
## 2006 - 1990 == 0  4.302e-01  3.323e-01   1.294 0.195505    
## 2007 - 1990 == 0  2.731e-01  2.959e-01   0.923 0.356128    
## 2010 - 1990 == 0  2.733e-01  2.959e-01   0.923 0.355759    
## 2014 - 1990 == 0  1.990e-01  2.959e-01   0.672 0.501280    
## 2015 - 1990 == 0  2.552e-01  2.959e-01   0.862 0.388444    
## 2016 - 1990 == 0 -7.334e-02  2.959e-01  -0.248 0.804239    
## 2017 - 1990 == 0  1.130e-01  2.959e-01   0.382 0.702495    
## 2018 - 1990 == 0  3.607e-02  2.959e-01   0.122 0.902982    
## 1993 - 1992 == 0  1.891e-01  3.593e-01   0.526 0.598668    
## 1994 - 1992 == 0  5.409e-01  3.299e-01   1.640 0.101072    
## 1995 - 1992 == 0  8.211e-01  3.299e-01   2.489 0.012816 *  
## 1997 - 1992 == 0  6.749e-01  3.037e-01   2.222 0.026279 *  
## 1998 - 1992 == 0  1.083e-01  3.639e-01   0.298 0.765943    
## 2000 - 1992 == 0  1.218e-01  3.299e-01   0.369 0.711899    
## 2001 - 1992 == 0  6.183e-02  3.640e-01   0.170 0.865097    
## 2002 - 1992 == 0  1.613e-01  3.299e-01   0.489 0.624923    
## 2003 - 1992 == 0  1.473e-01  3.299e-01   0.446 0.655271    
## 2004 - 1992 == 0  4.587e-01  3.593e-01   1.276 0.201794    
## 2005 - 1992 == 0  1.689e-01  3.299e-01   0.512 0.608585    
## 2006 - 1992 == 0  3.058e-01  3.640e-01   0.840 0.400832    
## 2007 - 1992 == 0  1.486e-01  3.299e-01   0.451 0.652322    
## 2010 - 1992 == 0  1.488e-01  3.299e-01   0.451 0.651863    
## 2014 - 1992 == 0  7.457e-02  3.299e-01   0.226 0.821170    
## 2015 - 1992 == 0  1.308e-01  3.299e-01   0.396 0.691787    
## 2016 - 1992 == 0 -1.978e-01  3.299e-01  -0.599 0.548866    
## 2017 - 1992 == 0 -1.140e-02  3.299e-01  -0.035 0.972444    
## 2018 - 1992 == 0 -8.835e-02  3.299e-01  -0.268 0.788850    
## 1994 - 1993 == 0  3.518e-01  3.299e-01   1.066 0.286235    
## 1995 - 1993 == 0  6.319e-01  3.299e-01   1.916 0.055420 .  
## 1997 - 1993 == 0  4.858e-01  3.037e-01   1.599 0.109733    
## 1998 - 1993 == 0 -8.078e-02  3.639e-01  -0.222 0.824342    
## 2000 - 1993 == 0 -6.729e-02  3.299e-01  -0.204 0.838387    
## 2001 - 1993 == 0 -1.273e-01  3.640e-01  -0.350 0.726547    
## 2002 - 1993 == 0 -2.784e-02  3.299e-01  -0.084 0.932756    
## 2003 - 1993 == 0 -4.184e-02  3.299e-01  -0.127 0.899089    
## 2004 - 1993 == 0  2.695e-01  3.593e-01   0.750 0.453170    
## 2005 - 1993 == 0 -2.018e-02  3.299e-01  -0.061 0.951225    
## 2006 - 1993 == 0  1.167e-01  3.640e-01   0.321 0.748571    
## 2007 - 1993 == 0 -4.049e-02  3.299e-01  -0.123 0.902325    
## 2010 - 1993 == 0 -4.028e-02  3.299e-01  -0.122 0.902829    
## 2014 - 1993 == 0 -1.145e-01  3.299e-01  -0.347 0.728424    
## 2015 - 1993 == 0 -5.834e-02  3.299e-01  -0.177 0.859640    
## 2016 - 1993 == 0 -3.869e-01  3.299e-01  -1.173 0.240907    
## 2017 - 1993 == 0 -2.005e-01  3.299e-01  -0.608 0.543316    
## 2018 - 1993 == 0 -2.775e-01  3.299e-01  -0.841 0.400310    
## 1995 - 1994 == 0  2.801e-01  2.934e-01   0.955 0.339666    
## 1997 - 1994 == 0  1.340e-01  2.627e-01   0.510 0.610048    
## 1998 - 1994 == 0 -4.326e-01  3.293e-01  -1.314 0.189004    
## 2000 - 1994 == 0 -4.191e-01  2.934e-01  -1.428 0.153157    
## 2001 - 1994 == 0 -4.791e-01  3.293e-01  -1.455 0.145753    
## 2002 - 1994 == 0 -3.796e-01  2.934e-01  -1.294 0.195662    
## 2003 - 1994 == 0 -3.936e-01  2.934e-01  -1.342 0.179685    
## 2004 - 1994 == 0 -8.227e-02  3.299e-01  -0.249 0.803077    
## 2005 - 1994 == 0 -3.720e-01  2.934e-01  -1.268 0.204829    
## 2006 - 1994 == 0 -2.352e-01  3.293e-01  -0.714 0.475227    
## 2007 - 1994 == 0 -3.923e-01  2.934e-01  -1.337 0.181181    
## 2010 - 1994 == 0 -3.921e-01  2.934e-01  -1.336 0.181415    
## 2014 - 1994 == 0 -4.664e-01  2.934e-01  -1.590 0.111933    
## 2015 - 1994 == 0 -4.102e-01  2.934e-01  -1.398 0.162122    
## 2016 - 1994 == 0 -7.387e-01  2.934e-01  -2.518 0.011809 *  
## 2017 - 1994 == 0 -5.523e-01  2.934e-01  -1.883 0.059758 .  
## 2018 - 1994 == 0 -6.293e-01  2.934e-01  -2.145 0.031963 *  
## 1997 - 1995 == 0 -1.462e-01  2.627e-01  -0.556 0.577902    
## 1998 - 1995 == 0 -7.127e-01  3.293e-01  -2.164 0.030454 *  
## 2000 - 1995 == 0 -6.992e-01  2.934e-01  -2.383 0.017158 *  
## 2001 - 1995 == 0 -7.592e-01  3.293e-01  -2.305 0.021151 *  
## 2002 - 1995 == 0 -6.598e-01  2.934e-01  -2.249 0.024523 *  
## 2003 - 1995 == 0 -6.738e-01  2.934e-01  -2.297 0.021644 *  
## 2004 - 1995 == 0 -3.624e-01  3.299e-01  -1.099 0.271978    
## 2005 - 1995 == 0 -6.521e-01  2.934e-01  -2.223 0.026233 *  
## 2006 - 1995 == 0 -5.153e-01  3.293e-01  -1.565 0.117681    
## 2007 - 1995 == 0 -6.724e-01  2.934e-01  -2.292 0.021908 *  
## 2010 - 1995 == 0 -6.722e-01  2.934e-01  -2.291 0.021950 *  
## 2014 - 1995 == 0 -7.465e-01  2.934e-01  -2.544 0.010947 *  
## 2015 - 1995 == 0 -6.903e-01  2.934e-01  -2.353 0.018633 *  
## 2016 - 1995 == 0 -1.019e+00  2.934e-01  -3.473 0.000515 ***
## 2017 - 1995 == 0 -8.325e-01  2.934e-01  -2.837 0.004548 ** 
## 2018 - 1995 == 0 -9.094e-01  2.934e-01  -3.100 0.001937 ** 
## 1998 - 1997 == 0 -5.666e-01  3.012e-01  -1.881 0.059930 .  
## 2000 - 1997 == 0 -5.531e-01  2.627e-01  -2.105 0.035250 *  
## 2001 - 1997 == 0 -6.131e-01  3.026e-01  -2.026 0.042793 *  
## 2002 - 1997 == 0 -5.136e-01  2.627e-01  -1.955 0.050548 .  
## 2003 - 1997 == 0 -5.276e-01  2.627e-01  -2.009 0.044580 *  
## 2004 - 1997 == 0 -2.162e-01  3.037e-01  -0.712 0.476505    
## 2005 - 1997 == 0 -5.060e-01  2.627e-01  -1.926 0.054086 .  
## 2006 - 1997 == 0 -3.691e-01  3.026e-01  -1.220 0.222592    
## 2007 - 1997 == 0 -5.263e-01  2.627e-01  -2.003 0.045128 *  
## 2010 - 1997 == 0 -5.261e-01  2.627e-01  -2.003 0.045214 *  
## 2014 - 1997 == 0 -6.003e-01  2.627e-01  -2.285 0.022289 *  
## 2015 - 1997 == 0 -5.441e-01  2.627e-01  -2.071 0.038320 *  
## 2016 - 1997 == 0 -8.727e-01  2.627e-01  -3.322 0.000893 ***
## 2017 - 1997 == 0 -6.863e-01  2.627e-01  -2.613 0.008984 ** 
## 2018 - 1997 == 0 -7.633e-01  2.627e-01  -2.906 0.003665 ** 
## 2000 - 1998 == 0  1.350e-02  3.293e-01   0.041 0.967314    
## 2001 - 1998 == 0 -4.651e-02  3.624e-01  -0.128 0.897898    
## 2002 - 1998 == 0  5.294e-02  3.293e-01   0.161 0.872281    
## 2003 - 1998 == 0  3.895e-02  3.293e-01   0.118 0.905866    
## 2004 - 1998 == 0  3.503e-01  3.639e-01   0.963 0.335748    
## 2005 - 1998 == 0  6.060e-02  3.293e-01   0.184 0.854005    
## 2006 - 1998 == 0  1.974e-01  3.624e-01   0.545 0.585909    
## 2007 - 1998 == 0  4.029e-02  3.293e-01   0.122 0.902623    
## 2010 - 1998 == 0  4.050e-02  3.293e-01   0.123 0.902117    
## 2014 - 1998 == 0 -3.377e-02  3.293e-01  -0.103 0.918333    
## 2015 - 1998 == 0  2.244e-02  3.293e-01   0.068 0.945668    
## 2016 - 1998 == 0 -3.061e-01  3.293e-01  -0.929 0.352655    
## 2017 - 1998 == 0 -1.197e-01  3.293e-01  -0.364 0.716183    
## 2018 - 1998 == 0 -1.967e-01  3.293e-01  -0.597 0.550356    
## 2001 - 2000 == 0 -6.000e-02  3.293e-01  -0.182 0.855439    
## 2002 - 2000 == 0  3.945e-02  2.934e-01   0.134 0.893039    
## 2003 - 2000 == 0  2.545e-02  2.934e-01   0.087 0.930874    
## 2004 - 2000 == 0  3.368e-01  3.299e-01   1.021 0.307251    
## 2005 - 2000 == 0  4.711e-02  2.934e-01   0.161 0.872442    
## 2006 - 2000 == 0  1.839e-01  3.293e-01   0.559 0.576492    
## 2007 - 2000 == 0  2.680e-02  2.934e-01   0.091 0.927222    
## 2010 - 2000 == 0  2.701e-02  2.934e-01   0.092 0.926653    
## 2014 - 2000 == 0 -4.726e-02  2.934e-01  -0.161 0.872018    
## 2015 - 2000 == 0  8.948e-03  2.934e-01   0.030 0.975669    
## 2016 - 2000 == 0 -3.196e-01  2.934e-01  -1.089 0.276009    
## 2017 - 2000 == 0 -1.332e-01  2.934e-01  -0.454 0.649751    
## 2018 - 2000 == 0 -2.102e-01  2.934e-01  -0.716 0.473746    
## 2002 - 2001 == 0  9.945e-02  3.293e-01   0.302 0.762680    
## 2003 - 2001 == 0  8.545e-02  3.293e-01   0.259 0.795283    
## 2004 - 2001 == 0  3.968e-01  3.640e-01   1.090 0.275579    
## 2005 - 2001 == 0  1.071e-01  3.293e-01   0.325 0.745021    
## 2006 - 2001 == 0  2.439e-01  3.593e-01   0.679 0.497203    
## 2007 - 2001 == 0  8.680e-02  3.293e-01   0.264 0.792126    
## 2010 - 2001 == 0  8.701e-02  3.293e-01   0.264 0.791634    
## 2014 - 2001 == 0  1.274e-02  3.293e-01   0.039 0.969150    
## 2015 - 2001 == 0  6.895e-02  3.293e-01   0.209 0.834173    
## 2016 - 2001 == 0 -2.596e-01  3.293e-01  -0.788 0.430569    
## 2017 - 2001 == 0 -7.323e-02  3.293e-01  -0.222 0.824043    
## 2018 - 2001 == 0 -1.502e-01  3.293e-01  -0.456 0.648388    
## 2003 - 2002 == 0 -1.400e-02  2.934e-01  -0.048 0.961943    
## 2004 - 2002 == 0  2.974e-01  3.299e-01   0.901 0.367360    
## 2005 - 2002 == 0  7.657e-03  2.934e-01   0.026 0.979180    
## 2006 - 2002 == 0  1.445e-01  3.293e-01   0.439 0.660853    
## 2007 - 2002 == 0 -1.265e-02  2.934e-01  -0.043 0.965607    
## 2010 - 2002 == 0 -1.244e-02  2.934e-01  -0.042 0.966177    
## 2014 - 2002 == 0 -8.671e-02  2.934e-01  -0.296 0.767570    
## 2015 - 2002 == 0 -3.050e-02  2.934e-01  -0.104 0.917201    
## 2016 - 2002 == 0 -3.590e-01  2.934e-01  -1.224 0.221032    
## 2017 - 2002 == 0 -1.727e-01  2.934e-01  -0.589 0.556151    
## 2018 - 2002 == 0 -2.496e-01  2.934e-01  -0.851 0.394848    
## 2004 - 2003 == 0  3.114e-01  3.299e-01   0.944 0.345240    
## 2005 - 2003 == 0  2.166e-02  2.934e-01   0.074 0.941160    
## 2006 - 2003 == 0  1.585e-01  3.293e-01   0.481 0.630344    
## 2007 - 2003 == 0  1.348e-03  2.934e-01   0.005 0.996333    
## 2010 - 2003 == 0  1.558e-03  2.934e-01   0.005 0.995762    
## 2014 - 2003 == 0 -7.271e-02  2.934e-01  -0.248 0.804258    
## 2015 - 2003 == 0 -1.650e-02  2.934e-01  -0.056 0.955146    
## 2016 - 2003 == 0 -3.450e-01  2.934e-01  -1.176 0.239566    
## 2017 - 2003 == 0 -1.587e-01  2.934e-01  -0.541 0.588609    
## 2018 - 2003 == 0 -2.356e-01  2.934e-01  -0.803 0.421892    
## 2005 - 2004 == 0 -2.897e-01  3.299e-01  -0.878 0.379824    
## 2006 - 2004 == 0 -1.529e-01  3.640e-01  -0.420 0.674443    
## 2007 - 2004 == 0 -3.100e-01  3.299e-01  -0.940 0.347333    
## 2010 - 2004 == 0 -3.098e-01  3.299e-01  -0.939 0.347659    
## 2014 - 2004 == 0 -3.841e-01  3.299e-01  -1.164 0.244313    
## 2015 - 2004 == 0 -3.279e-01  3.299e-01  -0.994 0.320280    
## 2016 - 2004 == 0 -6.564e-01  3.299e-01  -1.990 0.046616 *  
## 2017 - 2004 == 0 -4.701e-01  3.299e-01  -1.425 0.154198    
## 2018 - 2004 == 0 -5.470e-01  3.299e-01  -1.658 0.097294 .  
## 2006 - 2005 == 0  1.368e-01  3.293e-01   0.415 0.677785    
## 2007 - 2005 == 0 -2.031e-02  2.934e-01  -0.069 0.944817    
## 2010 - 2005 == 0 -2.010e-02  2.934e-01  -0.069 0.945387    
## 2014 - 2005 == 0 -9.437e-02  2.934e-01  -0.322 0.747716    
## 2015 - 2005 == 0 -3.816e-02  2.934e-01  -0.130 0.896520    
## 2016 - 2005 == 0 -3.667e-01  2.934e-01  -1.250 0.211342    
## 2017 - 2005 == 0 -1.803e-01  2.934e-01  -0.615 0.538775    
## 2018 - 2005 == 0 -2.573e-01  2.934e-01  -0.877 0.380511    
## 2007 - 2006 == 0 -1.571e-01  3.293e-01  -0.477 0.633257    
## 2010 - 2006 == 0 -1.569e-01  3.293e-01  -0.477 0.633711    
## 2014 - 2006 == 0 -2.312e-01  3.293e-01  -0.702 0.482664    
## 2015 - 2006 == 0 -1.750e-01  3.293e-01  -0.531 0.595178    
## 2016 - 2006 == 0 -5.035e-01  3.293e-01  -1.529 0.126285    
## 2017 - 2006 == 0 -3.172e-01  3.293e-01  -0.963 0.335524    
## 2018 - 2006 == 0 -3.941e-01  3.293e-01  -1.197 0.231423    
## 2010 - 2007 == 0  2.101e-04  2.934e-01   0.001 0.999429    
## 2014 - 2007 == 0 -7.406e-02  2.934e-01  -0.252 0.800704    
## 2015 - 2007 == 0 -1.785e-02  2.934e-01  -0.061 0.951485    
## 2016 - 2007 == 0 -3.464e-01  2.934e-01  -1.181 0.237734    
## 2017 - 2007 == 0 -1.600e-01  2.934e-01  -0.545 0.585445    
## 2018 - 2007 == 0 -2.370e-01  2.934e-01  -0.808 0.419241    
## 2014 - 2010 == 0 -7.427e-02  2.934e-01  -0.253 0.800151    
## 2015 - 2010 == 0 -1.806e-02  2.934e-01  -0.062 0.950915    
## 2016 - 2010 == 0 -3.466e-01  2.934e-01  -1.181 0.237450    
## 2017 - 2010 == 0 -1.602e-01  2.934e-01  -0.546 0.584952    
## 2018 - 2010 == 0 -2.372e-01  2.934e-01  -0.808 0.418829    
## 2015 - 2014 == 0  5.621e-02  2.934e-01   0.192 0.848060    
## 2016 - 2014 == 0 -2.723e-01  2.934e-01  -0.928 0.353287    
## 2017 - 2014 == 0 -8.597e-02  2.934e-01  -0.293 0.769512    
## 2018 - 2014 == 0 -1.629e-01  2.934e-01  -0.555 0.578688    
## 2016 - 2015 == 0 -3.285e-01  2.934e-01  -1.120 0.262788    
## 2017 - 2015 == 0 -1.422e-01  2.934e-01  -0.485 0.627955    
## 2018 - 2015 == 0 -2.191e-01  2.934e-01  -0.747 0.455126    
## 2017 - 2016 == 0  1.864e-01  2.934e-01   0.635 0.525286    
## 2018 - 2016 == 0  1.094e-01  2.934e-01   0.373 0.709201    
## 2018 - 2017 == 0 -7.695e-02  2.934e-01  -0.262 0.793098    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Univariate p values reported)

Model 4 plot (Massives, significant)

 Model4_All<-grid.arrange(massives_plot, model4_plot, ncol=2)

Aggregate data (Millepora)

  • Hierarchically aggregate by location
# Aggregate by Location
  aggr.location.mill <- aggregate(Millepora ~ YEAR+Month+Location, 
                        FUN=mean,data=cover)
  aggr.location.mill$Year_F<-as.factor(aggr.location.mill$YEAR)

Millepora model (5)

This model includes aggregated data from Chiriqui

  • Aggregated by location
  • YEAR is continuous
  • Location as a random factor

Model is NOT significant

# All years 1980_2018 
  Model5 <- lme(Millepora ~ YEAR, random = ~1|Location, data=aggr.location.mill)
  summary(Model5)
## Linear mixed-effects model fit by REML
##   Data: aggr.location.mill 
##        AIC      BIC    logLik
##   377.6839 387.4545 -184.8419
## 
## Random effects:
##  Formula: ~1 | Location
##         (Intercept) Residual
## StdDev:    1.036569 1.914402
## 
## Fixed effects:  Millepora ~ YEAR 
##                Value Std.Error DF   t-value p-value
## (Intercept) 57.58958  38.17441 83  1.508591  0.1352
## YEAR        -0.02853   0.01909 83 -1.494158  0.1389
##  Correlation: 
##      (Intr)
## YEAR -1    
## 
## Standardized Within-Group Residuals:
##         Min          Q1         Med          Q3         Max 
## -0.88787712 -0.19988893 -0.11320291  0.09071803  6.59088878 
## 
## Number of Observations: 87
## Number of Groups: 3
  anova(Model5)
  #plot(ranef(Model5))    # Symmetrical scatter effects around zero?
  #plot(Model5)           # plot residuals vs fitted
  #resnorm1 <- resid(Model5)
  #hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
  #coef.m1 <- as.data.frame(coef(summary(Model5)))    # Coefficients of the model
  
  #plot(Model5, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
  #plot(Model5, Millepora ~ fitted(.), abline = c(0,1))

Millepora model 6 (multiple comparisons between years)

This model includes data from Chiriqui * aggregated by location * Year is a factor * location as a random factor

# All years 1980_2018 
  Model6 <- lme(
    Millepora ~ -1 + Year_F, random = ~1|Location, data=aggr.location.mill)
  #summary(Model6)
  anova(Model6)

Millepora plots (non-significant models)

Aggregate data (all Scleractinians)

  • Hierarchically aggregate by location
# Aggregate by Location
  aggr.location.scl <- aggregate(All_Corals ~ YEAR+Month+Location, 
                        FUN=mean,data=cover)
  aggr.location.scl$Year_F<-as.factor(aggr.location.scl$YEAR)

All scleractinians (model 7)

This model includes aggregated data from Chiriqui

  • Aggregated by location
  • YEAR as a continuous variable
  • Location as a random factor

Model is significant

# All years 1980_2018 
  Model7 <- lme(All_Corals ~ YEAR, random = ~1|Location, data=aggr.location.scl)
  summary(Model7)
## Linear mixed-effects model fit by REML
##   Data: aggr.location.scl 
##        AIC     BIC    logLik
##   727.2946 737.112 -359.6473
## 
## Random effects:
##  Formula: ~1 | Location
##         (Intercept) Residual
## StdDev:    9.033042   14.216
## 
## Fixed effects:  All_Corals ~ YEAR 
##                  Value Std.Error DF   t-value p-value
## (Intercept) -3018.5300 280.78547 84 -10.75031       0
## YEAR            1.5216   0.14045 84  10.83406       0
##  Correlation: 
##      (Intr)
## YEAR -1    
## 
## Standardized Within-Group Residuals:
##        Min         Q1        Med         Q3        Max 
## -1.1579451 -0.6162544 -0.2954427  0.4970609  5.2973659 
## 
## Number of Observations: 88
## Number of Groups: 3
  anova(Model7)
  plot(ranef(Model7))    # Symmetrical scatter effects around zero?
  plot(Model7)           # plot residuals vs fitted
  resnorm1 <- resid(Model7)
  hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
  coef.m1 <- as.data.frame(coef(summary(Model7)))    # Coefficients of the model
  
  plot(Model7, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
  plot(Model7, All_Corals ~ fitted(.), abline = c(0,1))

Model 7 plot

Scleractinian_plot <- ggplot(aggr.location.scl, 
                             aes(x=YEAR, y=All_Corals)) +
  #geom_boxplot(aes(group=YEAR), outlier.shape = NA) +
  #stat_boxplot(aes(group=YEAR), geom = 'errorbar')+
  geom_point(aes(fill=factor(Location)),
                 shape = 21, colour = "black",
                 size = 2, stroke = 0.8, alpha=0.5) +
  geom_smooth(method = lm, se=FALSE, linetype = "dashed", colour="red")+
  geom_smooth(span = 0.3, se=T, colour="darkgray")+ 
  scale_y_continuous("Coral cover (%)", limits = c(-0.5, 80), expand = c(0,0))+
  scale_x_continuous("", limits = c(1979, 2019),
                     breaks = seq(1979, 2019, by=2), expand = c(0,0))+
  annotate("rect", xmin = 1982, xmax = 1983, 
           ymin = 0, ymax = 80,  alpha = .2, fill="gray")+
  annotate("rect", xmin = 1997, xmax = 1998, 
           ymin = 0, ymax = 80,  alpha = .2, fill="gray")+
  annotate("rect", xmin = 2015, xmax = 2016,
           ymin = 0, ymax = 80,  alpha = .2, fill="gray")

Scleractinian_plot + theme(legend.position = c(0.25, 0.8))

Scleractinians model 8 (multiple comparisons between years)

This model includes data from Chiriqui

  • Aggregated by location
  • Year as a factor
  • Location as a random factor
# All years 1980_2018 
  Model8 <- lme(
    All_Corals ~ -1 + Year_F, random = ~1|Location, data=aggr.location.scl)
  #summary(Model8)
  anova(Model8)
  plot(ranef(Model8))    # Symmetrical scatter effects around zero?
  plot(Model8)           # plot residuals vs fitted
  resnorm1 <- resid(Model8)
  hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
  coef.m1 <- as.data.frame(coef(summary(Model8)))    # Coefficients of the model
  
  plot(Model8, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
  plot(Model8, All_Corals ~ fitted(.), abline = c(0,1))
  
  # Multicomp
    Year_F.emm_scle<-emmeans(Model8, ~Year_F)
    #contrast(Year_F.emm, "tukey")
    year_groups_Scle<-cld(Year_F.emm_scle, by=NULL) # compact-letter display
    year_groups_Scle

Model 8 plot data

Model 8 plot

# Effect plot
  Model8_predictoin<-plot(emmeans(Model8, ~Year_F), comparisons = TRUE) +
      coord_flip(xlim = NULL, ylim = NULL, expand = TRUE) + theme_bw()+
    theme(axis.text.x = element_text(angle = 90)) + 
    ggtitle("Model 8 predictions (All scleractinians)")
 Model8_All<-grid.arrange(Scleractinian_plot, Model8_predictoin, ncol=2)

Summary:

  • Pretty much same as only Pocillopora …

  • 1980 is different from 1983-2001 -> Coral cover lose after 1981-82 ENSO
  • “Recovery” by 2002 (no differences between 1980 and 2002) uninterrupted until 2018 -> no significant cover loss in 1997-98 nor 2015-16
  • 1997 not different from 1998, 2000, 2001, 2003
  • 2015 not different from 2016, 2017, 2018

m.comp_sclera <- glht(Model8, linfct = mcp(Year_F = "Tukey"))
summary(m.comp_sclera, test = univariate())
## 
##   Simultaneous Tests for General Linear Hypotheses
## 
## Multiple Comparisons of Means: Tukey Contrasts
## 
## 
## Fit: lme.formula(fixed = All_Corals ~ -1 + Year_F, data = aggr.location.scl, 
##     random = ~1 | Location)
## 
## Linear Hypotheses:
##                  Estimate Std. Error z value Pr(>|z|)    
## 1983 - 1980 == 0 -28.6380    10.8980  -2.628 0.008593 ** 
## 1984 - 1980 == 0 -52.3502     9.5407  -5.487 4.09e-08 ***
## 1985 - 1980 == 0 -49.9089     9.3775  -5.322 1.03e-07 ***
## 1986 - 1980 == 0 -44.5140    11.8233  -3.765 0.000167 ***
## 1987 - 1980 == 0 -44.1940    11.8233  -3.738 0.000186 ***
## 1988 - 1980 == 0 -43.2755    11.8233  -3.660 0.000252 ***
## 1989 - 1980 == 0 -47.6223    10.8048  -4.408 1.05e-05 ***
## 1990 - 1980 == 0 -46.4883    10.8048  -4.303 1.69e-05 ***
## 1992 - 1980 == 0 -41.2590    11.8233  -3.490 0.000484 ***
## 1993 - 1980 == 0 -40.3945    11.8233  -3.417 0.000634 ***
## 1994 - 1980 == 0 -39.9292    10.8521  -3.679 0.000234 ***
## 1995 - 1980 == 0 -31.0275    10.8521  -2.859 0.004248 ** 
## 1997 - 1980 == 0 -28.4906     9.9890  -2.852 0.004342 ** 
## 1998 - 1980 == 0 -30.6310    11.9675  -2.560 0.010482 *  
## 2000 - 1980 == 0 -26.1579    10.8521  -2.410 0.015935 *  
## 2001 - 1980 == 0 -25.4153    11.9683  -2.124 0.033708 *  
## 2002 - 1980 == 0 -16.7682    10.8521  -1.545 0.122309    
## 2003 - 1980 == 0 -14.4000    10.8521  -1.327 0.184532    
## 2004 - 1980 == 0  -8.6560    11.8233  -0.732 0.464099    
## 2005 - 1980 == 0 -10.8151    10.8521  -0.997 0.318965    
## 2006 - 1980 == 0  -2.2793    11.9683  -0.190 0.848958    
## 2007 - 1980 == 0  -7.4482    10.8521  -0.686 0.492499    
## 2010 - 1980 == 0  -2.4605    10.8521  -0.227 0.820636    
## 2014 - 1980 == 0   0.5400    10.8521   0.050 0.960310    
## 2015 - 1980 == 0   1.9508    10.8521   0.180 0.857339    
## 2016 - 1980 == 0  -6.1193    10.8521  -0.564 0.572835    
## 2017 - 1980 == 0   8.8441    10.8521   0.815 0.415091    
## 2018 - 1980 == 0  10.3253    10.8521   0.951 0.341372    
## 1984 - 1983 == 0 -23.7122     8.5587  -2.771 0.005596 ** 
## 1985 - 1983 == 0 -21.2709     8.3179  -2.557 0.010551 *  
## 1986 - 1983 == 0 -15.8760    10.8980  -1.457 0.145176    
## 1987 - 1983 == 0 -15.5560    10.8980  -1.427 0.153459    
## 1988 - 1983 == 0 -14.6375    10.8980  -1.343 0.179227    
## 1989 - 1983 == 0 -18.9844     9.8609  -1.925 0.054202 .  
## 1990 - 1983 == 0 -17.8504     9.8609  -1.810 0.070261 .  
## 1992 - 1983 == 0 -12.6210    10.8980  -1.158 0.246821    
## 1993 - 1983 == 0 -11.7565    10.8980  -1.079 0.280686    
## 1994 - 1983 == 0 -11.2912     9.8365  -1.148 0.251013    
## 1995 - 1983 == 0  -2.3895     9.8365  -0.243 0.808065    
## 1997 - 1983 == 0   0.1474     8.8239   0.017 0.986676    
## 1998 - 1983 == 0  -1.9930    10.9518  -0.182 0.855597    
## 2000 - 1983 == 0   2.4801     9.8365   0.252 0.800939    
## 2001 - 1983 == 0   3.2227    11.1584   0.289 0.772721    
## 2002 - 1983 == 0  11.8698     9.8365   1.207 0.227544    
## 2003 - 1983 == 0  14.2380     9.8365   1.447 0.147766    
## 2004 - 1983 == 0  19.9820    10.8980   1.834 0.066721 .  
## 2005 - 1983 == 0  17.8229     9.8365   1.812 0.069999 .  
## 2006 - 1983 == 0  26.3586    11.1584   2.362 0.018165 *  
## 2007 - 1983 == 0  21.1898     9.8365   2.154 0.031225 *  
## 2010 - 1983 == 0  26.1775     9.8365   2.661 0.007785 ** 
## 2014 - 1983 == 0  29.1780     9.8365   2.966 0.003014 ** 
## 2015 - 1983 == 0  30.5888     9.8365   3.110 0.001873 ** 
## 2016 - 1983 == 0  22.5187     9.8365   2.289 0.022062 *  
## 2017 - 1983 == 0  37.4821     9.8365   3.811 0.000139 ***
## 2018 - 1983 == 0  38.9633     9.8365   3.961 7.46e-05 ***
## 1985 - 1984 == 0   2.4413     6.1277   0.398 0.690334    
## 1986 - 1984 == 0   7.8362     9.5407   0.821 0.411454    
## 1987 - 1984 == 0   8.1562     9.5407   0.855 0.392619    
## 1988 - 1984 == 0   9.0747     9.5407   0.951 0.341529    
## 1989 - 1984 == 0   4.7278     8.1790   0.578 0.563237    
## 1990 - 1984 == 0   5.8618     8.1790   0.717 0.473567    
## 1992 - 1984 == 0  11.0912     9.5407   1.163 0.245030    
## 1993 - 1984 == 0  11.9557     9.5407   1.253 0.210163    
## 1994 - 1984 == 0  12.4209     8.3063   1.495 0.134820    
## 1995 - 1984 == 0  21.3227     8.3063   2.567 0.010257 *  
## 1997 - 1984 == 0  23.8595     7.1871   3.320 0.000901 ***
## 1998 - 1984 == 0  21.7191     9.8014   2.216 0.026697 *  
## 2000 - 1984 == 0  26.1923     8.3063   3.153 0.001614 ** 
## 2001 - 1984 == 0  26.9349     9.6352   2.795 0.005183 ** 
## 2002 - 1984 == 0  35.5820     8.3063   4.284 1.84e-05 ***
## 2003 - 1984 == 0  37.9502     8.3063   4.569 4.90e-06 ***
## 2004 - 1984 == 0  43.6942     9.5407   4.580 4.66e-06 ***
## 2005 - 1984 == 0  41.5351     8.3063   5.000 5.72e-07 ***
## 2006 - 1984 == 0  50.0708     9.6352   5.197 2.03e-07 ***
## 2007 - 1984 == 0  44.9019     8.3063   5.406 6.45e-08 ***
## 2010 - 1984 == 0  49.8897     8.3063   6.006 1.90e-09 ***
## 2014 - 1984 == 0  52.8902     8.3063   6.367 1.92e-10 ***
## 2015 - 1984 == 0  54.3010     8.3063   6.537 6.26e-11 ***
## 2016 - 1984 == 0  46.2308     8.3063   5.566 2.61e-08 ***
## 2017 - 1984 == 0  61.1943     8.3063   7.367 1.74e-13 ***
## 2018 - 1984 == 0  62.6755     8.3063   7.546 4.51e-14 ***
## 1986 - 1985 == 0   5.3949     9.3775   0.575 0.565088    
## 1987 - 1985 == 0   5.7149     9.3775   0.609 0.542243    
## 1988 - 1985 == 0   6.6334     9.3775   0.707 0.479335    
## 1989 - 1985 == 0   2.2865     8.0083   0.286 0.775246    
## 1990 - 1985 == 0   3.4205     8.0083   0.427 0.669290    
## 1992 - 1985 == 0   8.6499     9.3775   0.922 0.356315    
## 1993 - 1985 == 0   9.5144     9.3775   1.015 0.310298    
## 1994 - 1985 == 0   9.9797     8.1185   1.229 0.218976    
## 1995 - 1985 == 0  18.8814     8.1185   2.326 0.020033 *  
## 1997 - 1985 == 0  21.4182     6.9551   3.079 0.002074 ** 
## 1998 - 1985 == 0  19.2779     9.6175   2.004 0.045022 *  
## 2000 - 1985 == 0  23.7510     8.1185   2.926 0.003438 ** 
## 2001 - 1985 == 0  24.4936     9.4995   2.578 0.009926 ** 
## 2002 - 1985 == 0  33.1407     8.1185   4.082 4.46e-05 ***
## 2003 - 1985 == 0  35.5089     8.1185   4.374 1.22e-05 ***
## 2004 - 1985 == 0  41.2529     9.3775   4.399 1.09e-05 ***
## 2005 - 1985 == 0  39.0938     8.1185   4.815 1.47e-06 ***
## 2006 - 1985 == 0  47.6295     9.4995   5.014 5.33e-07 ***
## 2007 - 1985 == 0  42.4607     8.1185   5.230 1.69e-07 ***
## 2010 - 1985 == 0  47.4484     8.1185   5.845 5.08e-09 ***
## 2014 - 1985 == 0  50.4489     8.1185   6.214 5.16e-10 ***
## 2015 - 1985 == 0  51.8597     8.1185   6.388 1.68e-10 ***
## 2016 - 1985 == 0  43.7896     8.1185   5.394 6.90e-08 ***
## 2017 - 1985 == 0  58.7530     8.1185   7.237 4.59e-13 ***
## 2018 - 1985 == 0  60.2342     8.1185   7.419 1.18e-13 ***
## 1987 - 1986 == 0   0.3200    11.8233   0.027 0.978408    
## 1988 - 1986 == 0   1.2385    11.8233   0.105 0.916573    
## 1989 - 1986 == 0  -3.1083    10.8048  -0.288 0.773591    
## 1990 - 1986 == 0  -1.9743    10.8048  -0.183 0.855012    
## 1992 - 1986 == 0   3.2550    11.8233   0.275 0.783083    
## 1993 - 1986 == 0   4.1195    11.8233   0.348 0.727523    
## 1994 - 1986 == 0   4.5848    10.8521   0.422 0.672676    
## 1995 - 1986 == 0  13.4865    10.8521   1.243 0.213959    
## 1997 - 1986 == 0  16.0234     9.9890   1.604 0.108690    
## 1998 - 1986 == 0  13.8830    11.9675   1.160 0.246026    
## 2000 - 1986 == 0  18.3561    10.8521   1.691 0.090746 .  
## 2001 - 1986 == 0  19.0987    11.9683   1.596 0.110539    
## 2002 - 1986 == 0  27.7458    10.8521   2.557 0.010566 *  
## 2003 - 1986 == 0  30.1140    10.8521   2.775 0.005521 ** 
## 2004 - 1986 == 0  35.8580    11.8233   3.033 0.002423 ** 
## 2005 - 1986 == 0  33.6989    10.8521   3.105 0.001901 ** 
## 2006 - 1986 == 0  42.2347    11.9683   3.529 0.000417 ***
## 2007 - 1986 == 0  37.0658    10.8521   3.416 0.000637 ***
## 2010 - 1986 == 0  42.0535    10.8521   3.875 0.000107 ***
## 2014 - 1986 == 0  45.0540    10.8521   4.152 3.30e-05 ***
## 2015 - 1986 == 0  46.4648    10.8521   4.282 1.86e-05 ***
## 2016 - 1986 == 0  38.3947    10.8521   3.538 0.000403 ***
## 2017 - 1986 == 0  53.3581    10.8521   4.917 8.80e-07 ***
## 2018 - 1986 == 0  54.8393    10.8521   5.053 4.34e-07 ***
## 1988 - 1987 == 0   0.9185    11.8233   0.078 0.938078    
## 1989 - 1987 == 0  -3.4283    10.8048  -0.317 0.751019    
## 1990 - 1987 == 0  -2.2943    10.8048  -0.212 0.831839    
## 1992 - 1987 == 0   2.9350    11.8233   0.248 0.803950    
## 1993 - 1987 == 0   3.7995    11.8233   0.321 0.747940    
## 1994 - 1987 == 0   4.2648    10.8521   0.393 0.694327    
## 1995 - 1987 == 0  13.1665    10.8521   1.213 0.225028    
## 1997 - 1987 == 0  15.7034     9.9890   1.572 0.115934    
## 1998 - 1987 == 0  13.5630    11.9675   1.133 0.257082    
## 2000 - 1987 == 0  18.0361    10.8521   1.662 0.096515 .  
## 2001 - 1987 == 0  18.7787    11.9683   1.569 0.116639    
## 2002 - 1987 == 0  27.4258    10.8521   2.527 0.011497 *  
## 2003 - 1987 == 0  29.7940    10.8521   2.745 0.006043 ** 
## 2004 - 1987 == 0  35.5380    11.8233   3.006 0.002649 ** 
## 2005 - 1987 == 0  33.3789    10.8521   3.076 0.002099 ** 
## 2006 - 1987 == 0  41.9147    11.9683   3.502 0.000462 ***
## 2007 - 1987 == 0  36.7458    10.8521   3.386 0.000709 ***
## 2010 - 1987 == 0  41.7335    10.8521   3.846 0.000120 ***
## 2014 - 1987 == 0  44.7340    10.8521   4.122 3.75e-05 ***
## 2015 - 1987 == 0  46.1448    10.8521   4.252 2.12e-05 ***
## 2016 - 1987 == 0  38.0747    10.8521   3.509 0.000451 ***
## 2017 - 1987 == 0  53.0381    10.8521   4.887 1.02e-06 ***
## 2018 - 1987 == 0  54.5193    10.8521   5.024 5.06e-07 ***
## 1989 - 1988 == 0  -4.3468    10.8048  -0.402 0.687460    
## 1990 - 1988 == 0  -3.2128    10.8048  -0.297 0.766198    
## 1992 - 1988 == 0   2.0165    11.8233   0.171 0.864575    
## 1993 - 1988 == 0   2.8810    11.8233   0.244 0.807485    
## 1994 - 1988 == 0   3.3463    10.8521   0.308 0.757814    
## 1995 - 1988 == 0  12.2480    10.8521   1.129 0.259055    
## 1997 - 1988 == 0  14.7849     9.9890   1.480 0.138841    
## 1998 - 1988 == 0  12.6445    11.9675   1.057 0.290709    
## 2000 - 1988 == 0  17.1176    10.8521   1.577 0.114714    
## 2001 - 1988 == 0  17.8602    11.9683   1.492 0.135622    
## 2002 - 1988 == 0  26.5073    10.8521   2.443 0.014582 *  
## 2003 - 1988 == 0  28.8755    10.8521   2.661 0.007795 ** 
## 2004 - 1988 == 0  34.6195    11.8233   2.928 0.003411 ** 
## 2005 - 1988 == 0  32.4604    10.8521   2.991 0.002779 ** 
## 2006 - 1988 == 0  40.9962    11.9683   3.425 0.000614 ***
## 2007 - 1988 == 0  35.8273    10.8521   3.301 0.000962 ***
## 2010 - 1988 == 0  40.8150    10.8521   3.761 0.000169 ***
## 2014 - 1988 == 0  43.8155    10.8521   4.038 5.40e-05 ***
## 2015 - 1988 == 0  45.2263    10.8521   4.168 3.08e-05 ***
## 2016 - 1988 == 0  37.1562    10.8521   3.424 0.000617 ***
## 2017 - 1988 == 0  52.1196    10.8521   4.803 1.57e-06 ***
## 2018 - 1988 == 0  53.6008    10.8521   4.939 7.84e-07 ***
## 1990 - 1989 == 0   1.1340     9.6537   0.117 0.906489    
## 1992 - 1989 == 0   6.3633    10.8048   0.589 0.555905    
## 1993 - 1989 == 0   7.2278    10.8048   0.669 0.503531    
## 1994 - 1989 == 0   7.6931     9.7323   0.790 0.429254    
## 1995 - 1989 == 0  16.5948     9.7323   1.705 0.088172 .  
## 1997 - 1989 == 0  19.1317     8.7768   2.180 0.029272 *  
## 1998 - 1989 == 0  16.9913    10.9967   1.545 0.122316    
## 2000 - 1989 == 0  21.4644     9.7323   2.205 0.027421 *  
## 2001 - 1989 == 0  22.2071    10.9284   2.032 0.042149 *  
## 2002 - 1989 == 0  30.8541     9.7323   3.170 0.001523 ** 
## 2003 - 1989 == 0  33.2224     9.7323   3.414 0.000641 ***
## 2004 - 1989 == 0  38.9663    10.8048   3.606 0.000310 ***
## 2005 - 1989 == 0  36.8073     9.7323   3.782 0.000156 ***
## 2006 - 1989 == 0  45.3430    10.9284   4.149 3.34e-05 ***
## 2007 - 1989 == 0  40.1741     9.7323   4.128 3.66e-05 ***
## 2010 - 1989 == 0  45.1619     9.7323   4.640 3.48e-06 ***
## 2014 - 1989 == 0  48.1624     9.7323   4.949 7.47e-07 ***
## 2015 - 1989 == 0  49.5731     9.7323   5.094 3.51e-07 ***
## 2016 - 1989 == 0  41.5030     9.7323   4.264 2.00e-05 ***
## 2017 - 1989 == 0  56.4664     9.7323   5.802 6.56e-09 ***
## 2018 - 1989 == 0  57.9477     9.7323   5.954 2.61e-09 ***
## 1992 - 1990 == 0   5.2293    10.8048   0.484 0.628399    
## 1993 - 1990 == 0   6.0938    10.8048   0.564 0.572760    
## 1994 - 1990 == 0   6.5591     9.7323   0.674 0.500343    
## 1995 - 1990 == 0  15.4608     9.7323   1.589 0.112150    
## 1997 - 1990 == 0  17.9977     8.7768   2.051 0.040306 *  
## 1998 - 1990 == 0  15.8573    10.9967   1.442 0.149301    
## 2000 - 1990 == 0  20.3304     9.7323   2.089 0.036712 *  
## 2001 - 1990 == 0  21.0731    10.9284   1.928 0.053820 .  
## 2002 - 1990 == 0  29.7201     9.7323   3.054 0.002260 ** 
## 2003 - 1990 == 0  32.0884     9.7323   3.297 0.000977 ***
## 2004 - 1990 == 0  37.8323    10.8048   3.501 0.000463 ***
## 2005 - 1990 == 0  35.6733     9.7323   3.665 0.000247 ***
## 2006 - 1990 == 0  44.2090    10.9284   4.045 5.23e-05 ***
## 2007 - 1990 == 0  39.0401     9.7323   4.011 6.04e-05 ***
## 2010 - 1990 == 0  44.0279     9.7323   4.524 6.07e-06 ***
## 2014 - 1990 == 0  47.0284     9.7323   4.832 1.35e-06 ***
## 2015 - 1990 == 0  48.4391     9.7323   4.977 6.45e-07 ***
## 2016 - 1990 == 0  40.3690     9.7323   4.148 3.36e-05 ***
## 2017 - 1990 == 0  55.3324     9.7323   5.685 1.30e-08 ***
## 2018 - 1990 == 0  56.8137     9.7323   5.838 5.30e-09 ***
## 1993 - 1992 == 0   0.8645    11.8233   0.073 0.941712    
## 1994 - 1992 == 0   1.3298    10.8521   0.123 0.902475    
## 1995 - 1992 == 0  10.2315    10.8521   0.943 0.345777    
## 1997 - 1992 == 0  12.7684     9.9890   1.278 0.201162    
## 1998 - 1992 == 0  10.6280    11.9675   0.888 0.374504    
## 2000 - 1992 == 0  15.1011    10.8521   1.392 0.164063    
## 2001 - 1992 == 0  15.8437    11.9683   1.324 0.185567    
## 2002 - 1992 == 0  24.4908    10.8521   2.257 0.024022 *  
## 2003 - 1992 == 0  26.8590    10.8521   2.475 0.013323 *  
## 2004 - 1992 == 0  32.6030    11.8233   2.758 0.005824 ** 
## 2005 - 1992 == 0  30.4439    10.8521   2.805 0.005026 ** 
## 2006 - 1992 == 0  38.9797    11.9683   3.257 0.001126 ** 
## 2007 - 1992 == 0  33.8108    10.8521   3.116 0.001836 ** 
## 2010 - 1992 == 0  38.7985    10.8521   3.575 0.000350 ***
## 2014 - 1992 == 0  41.7990    10.8521   3.852 0.000117 ***
## 2015 - 1992 == 0  43.2098    10.8521   3.982 6.84e-05 ***
## 2016 - 1992 == 0  35.1397    10.8521   3.238 0.001203 ** 
## 2017 - 1992 == 0  50.1031    10.8521   4.617 3.90e-06 ***
## 2018 - 1992 == 0  51.5843    10.8521   4.753 2.00e-06 ***
## 1994 - 1993 == 0   0.4653    10.8521   0.043 0.965802    
## 1995 - 1993 == 0   9.3670    10.8521   0.863 0.388055    
## 1997 - 1993 == 0  11.9039     9.9890   1.192 0.233378    
## 1998 - 1993 == 0   9.7635    11.9675   0.816 0.414596    
## 2000 - 1993 == 0  14.2366    10.8521   1.312 0.189562    
## 2001 - 1993 == 0  14.9792    11.9683   1.252 0.210724    
## 2002 - 1993 == 0  23.6263    10.8521   2.177 0.029472 *  
## 2003 - 1993 == 0  25.9945    10.8521   2.395 0.016605 *  
## 2004 - 1993 == 0  31.7385    11.8233   2.684 0.007266 ** 
## 2005 - 1993 == 0  29.5794    10.8521   2.726 0.006417 ** 
## 2006 - 1993 == 0  38.1152    11.9683   3.185 0.001449 ** 
## 2007 - 1993 == 0  32.9463    10.8521   3.036 0.002398 ** 
## 2010 - 1993 == 0  37.9340    10.8521   3.496 0.000473 ***
## 2014 - 1993 == 0  40.9345    10.8521   3.772 0.000162 ***
## 2015 - 1993 == 0  42.3453    10.8521   3.902 9.54e-05 ***
## 2016 - 1993 == 0  34.2752    10.8521   3.158 0.001586 ** 
## 2017 - 1993 == 0  49.2386    10.8521   4.537 5.70e-06 ***
## 2018 - 1993 == 0  50.7198    10.8521   4.674 2.96e-06 ***
## 1995 - 1994 == 0   8.9017     9.6537   0.922 0.356472    
## 1997 - 1994 == 0  11.4386     8.6427   1.323 0.185670    
## 1998 - 1994 == 0   9.2982    10.8340   0.858 0.390760    
## 2000 - 1994 == 0  13.7713     9.6537   1.427 0.153713    
## 2001 - 1994 == 0  14.5140    10.8343   1.340 0.180366    
## 2002 - 1994 == 0  23.1610     9.6537   2.399 0.016431 *  
## 2003 - 1994 == 0  25.5292     9.6537   2.645 0.008181 ** 
## 2004 - 1994 == 0  31.2732    10.8521   2.882 0.003955 ** 
## 2005 - 1994 == 0  29.1142     9.6537   3.016 0.002562 ** 
## 2006 - 1994 == 0  37.6499    10.8343   3.475 0.000511 ***
## 2007 - 1994 == 0  32.4810     9.6537   3.365 0.000766 ***
## 2010 - 1994 == 0  37.4688     9.6537   3.881 0.000104 ***
## 2014 - 1994 == 0  40.4693     9.6537   4.192 2.76e-05 ***
## 2015 - 1994 == 0  41.8800     9.6537   4.338 1.44e-05 ***
## 2016 - 1994 == 0  33.8099     9.6537   3.502 0.000461 ***
## 2017 - 1994 == 0  48.7733     9.6537   5.052 4.37e-07 ***
## 2018 - 1994 == 0  50.2545     9.6537   5.206 1.93e-07 ***
## 1997 - 1995 == 0   2.5369     8.6427   0.294 0.769119    
## 1998 - 1995 == 0   0.3965    10.8340   0.037 0.970807    
## 2000 - 1995 == 0   4.8696     9.6537   0.504 0.613959    
## 2001 - 1995 == 0   5.6122    10.8343   0.518 0.604454    
## 2002 - 1995 == 0  14.2593     9.6537   1.477 0.139653    
## 2003 - 1995 == 0  16.6275     9.6537   1.722 0.084997 .  
## 2004 - 1995 == 0  22.3715    10.8521   2.061 0.039256 *  
## 2005 - 1995 == 0  20.2124     9.6537   2.094 0.036282 *  
## 2006 - 1995 == 0  28.7482    10.8343   2.653 0.007968 ** 
## 2007 - 1995 == 0  23.5793     9.6537   2.443 0.014585 *  
## 2010 - 1995 == 0  28.5670     9.6537   2.959 0.003085 ** 
## 2014 - 1995 == 0  31.5675     9.6537   3.270 0.001075 ** 
## 2015 - 1995 == 0  32.9783     9.6537   3.416 0.000635 ***
## 2016 - 1995 == 0  24.9082     9.6537   2.580 0.009875 ** 
## 2017 - 1995 == 0  39.8716     9.6537   4.130 3.62e-05 ***
## 2018 - 1995 == 0  41.3528     9.6537   4.284 1.84e-05 ***
## 1998 - 1997 == 0  -2.1404     9.9082  -0.216 0.828970    
## 2000 - 1997 == 0   2.3327     8.6427   0.270 0.787230    
## 2001 - 1997 == 0   3.0754     9.9541   0.309 0.757356    
## 2002 - 1997 == 0  11.7224     8.6427   1.356 0.174991    
## 2003 - 1997 == 0  14.0906     8.6427   1.630 0.103027    
## 2004 - 1997 == 0  19.8346     9.9890   1.986 0.047072 *  
## 2005 - 1997 == 0  17.6756     8.6427   2.045 0.040841 *  
## 2006 - 1997 == 0  26.2113     9.9541   2.633 0.008458 ** 
## 2007 - 1997 == 0  21.0424     8.6427   2.435 0.014904 *  
## 2010 - 1997 == 0  26.0302     8.6427   3.012 0.002597 ** 
## 2014 - 1997 == 0  29.0307     8.6427   3.359 0.000782 ***
## 2015 - 1997 == 0  30.4414     8.6427   3.522 0.000428 ***
## 2016 - 1997 == 0  22.3713     8.6427   2.588 0.009640 ** 
## 2017 - 1997 == 0  37.3347     8.6427   4.320 1.56e-05 ***
## 2018 - 1997 == 0  38.8160     8.6427   4.491 7.08e-06 ***
## 2000 - 1998 == 0   4.4731    10.8340   0.413 0.679697    
## 2001 - 1998 == 0   5.2158    11.9191   0.438 0.661678    
## 2002 - 1998 == 0  13.8628    10.8340   1.280 0.200699    
## 2003 - 1998 == 0  16.2310    10.8340   1.498 0.134094    
## 2004 - 1998 == 0  21.9750    11.9675   1.836 0.066325 .  
## 2005 - 1998 == 0  19.8159    10.8340   1.829 0.067393 .  
## 2006 - 1998 == 0  28.3517    11.9191   2.379 0.017375 *  
## 2007 - 1998 == 0  23.1828    10.8340   2.140 0.032370 *  
## 2010 - 1998 == 0  28.1705    10.8340   2.600 0.009317 ** 
## 2014 - 1998 == 0  31.1711    10.8340   2.877 0.004013 ** 
## 2015 - 1998 == 0  32.5818    10.8340   3.007 0.002635 ** 
## 2016 - 1998 == 0  24.5117    10.8340   2.262 0.023668 *  
## 2017 - 1998 == 0  39.4751    10.8340   3.644 0.000269 ***
## 2018 - 1998 == 0  40.9563    10.8340   3.780 0.000157 ***
## 2001 - 2000 == 0   0.7426    10.8343   0.069 0.945352    
## 2002 - 2000 == 0   9.3897     9.6537   0.973 0.330725    
## 2003 - 2000 == 0  11.7579     9.6537   1.218 0.223234    
## 2004 - 2000 == 0  17.5019    10.8521   1.613 0.106796    
## 2005 - 2000 == 0  15.3428     9.6537   1.589 0.111987    
## 2006 - 2000 == 0  23.8785    10.8343   2.204 0.027526 *  
## 2007 - 2000 == 0  18.7097     9.6537   1.938 0.052612 .  
## 2010 - 2000 == 0  23.6974     9.6537   2.455 0.014098 *  
## 2014 - 2000 == 0  26.6979     9.6537   2.766 0.005682 ** 
## 2015 - 2000 == 0  28.1087     9.6537   2.912 0.003595 ** 
## 2016 - 2000 == 0  20.0386     9.6537   2.076 0.037917 *  
## 2017 - 2000 == 0  35.0020     9.6537   3.626 0.000288 ***
## 2018 - 2000 == 0  36.4832     9.6537   3.779 0.000157 ***
## 2002 - 2001 == 0   8.6471    10.8343   0.798 0.424803    
## 2003 - 2001 == 0  11.0153    10.8343   1.017 0.309296    
## 2004 - 2001 == 0  16.7593    11.9683   1.400 0.161422    
## 2005 - 2001 == 0  14.6002    10.8343   1.348 0.177792    
## 2006 - 2001 == 0  23.1359    11.8233   1.957 0.050370 .  
## 2007 - 2001 == 0  17.9670    10.8343   1.658 0.097248 .  
## 2010 - 2001 == 0  22.9548    10.8343   2.119 0.034115 *  
## 2014 - 2001 == 0  25.9553    10.8343   2.396 0.016591 *  
## 2015 - 2001 == 0  27.3661    10.8343   2.526 0.011541 *  
## 2016 - 2001 == 0  19.2959    10.8343   1.781 0.074912 .  
## 2017 - 2001 == 0  34.2594    10.8343   3.162 0.001566 ** 
## 2018 - 2001 == 0  35.7406    10.8343   3.299 0.000971 ***
## 2003 - 2002 == 0   2.3682     9.6537   0.245 0.806211    
## 2004 - 2002 == 0   8.1122    10.8521   0.748 0.454748    
## 2005 - 2002 == 0   5.9531     9.6537   0.617 0.537453    
## 2006 - 2002 == 0  14.4889    10.8343   1.337 0.181121    
## 2007 - 2002 == 0   9.3200     9.6537   0.965 0.334328    
## 2010 - 2002 == 0  14.3077     9.6537   1.482 0.138313    
## 2014 - 2002 == 0  17.3082     9.6537   1.793 0.072986 .  
## 2015 - 2002 == 0  18.7190     9.6537   1.939 0.052495 .  
## 2016 - 2002 == 0  10.6489     9.6537   1.103 0.269987    
## 2017 - 2002 == 0  25.6123     9.6537   2.653 0.007975 ** 
## 2018 - 2002 == 0  27.0935     9.6537   2.807 0.005008 ** 
## 2004 - 2003 == 0   5.7440    10.8521   0.529 0.596600    
## 2005 - 2003 == 0   3.5849     9.6537   0.371 0.710375    
## 2006 - 2003 == 0  12.1206    10.8343   1.119 0.263257    
## 2007 - 2003 == 0   6.9518     9.6537   0.720 0.471454    
## 2010 - 2003 == 0  11.9395     9.6537   1.237 0.216167    
## 2014 - 2003 == 0  14.9400     9.6537   1.548 0.121718    
## 2015 - 2003 == 0  16.3508     9.6537   1.694 0.090315 .  
## 2016 - 2003 == 0   8.2807     9.6537   0.858 0.391017    
## 2017 - 2003 == 0  23.2441     9.6537   2.408 0.016049 *  
## 2018 - 2003 == 0  24.7253     9.6537   2.561 0.010430 *  
## 2005 - 2004 == 0  -2.1591    10.8521  -0.199 0.842298    
## 2006 - 2004 == 0   6.3767    11.9683   0.533 0.594175    
## 2007 - 2004 == 0   1.2078    10.8521   0.111 0.911383    
## 2010 - 2004 == 0   6.1955    10.8521   0.571 0.568064    
## 2014 - 2004 == 0   9.1960    10.8521   0.847 0.396774    
## 2015 - 2004 == 0  10.6068    10.8521   0.977 0.328373    
## 2016 - 2004 == 0   2.5367    10.8521   0.234 0.815178    
## 2017 - 2004 == 0  17.5001    10.8521   1.613 0.106832    
## 2018 - 2004 == 0  18.9813    10.8521   1.749 0.080275 .  
## 2006 - 2005 == 0   8.5357    10.8343   0.788 0.430789    
## 2007 - 2005 == 0   3.3668     9.6537   0.349 0.727267    
## 2010 - 2005 == 0   8.3546     9.6537   0.865 0.386801    
## 2014 - 2005 == 0  11.3551     9.6537   1.176 0.239495    
## 2015 - 2005 == 0  12.7659     9.6537   1.322 0.186040    
## 2016 - 2005 == 0   4.6958     9.6537   0.486 0.626667    
## 2017 - 2005 == 0  19.6592     9.6537   2.036 0.041706 *  
## 2018 - 2005 == 0  21.1404     9.6537   2.190 0.028533 *  
## 2007 - 2006 == 0  -5.1689    10.8343  -0.477 0.633302    
## 2010 - 2006 == 0  -0.1811    10.8343  -0.017 0.986662    
## 2014 - 2006 == 0   2.8194    10.8343   0.260 0.794688    
## 2015 - 2006 == 0   4.2301    10.8343   0.390 0.696211    
## 2016 - 2006 == 0  -3.8400    10.8343  -0.354 0.723020    
## 2017 - 2006 == 0  11.1235    10.8343   1.027 0.304568    
## 2018 - 2006 == 0  12.6047    10.8343   1.163 0.244667    
## 2010 - 2007 == 0   4.9878     9.6537   0.517 0.605387    
## 2014 - 2007 == 0   7.9883     9.6537   0.827 0.407962    
## 2015 - 2007 == 0   9.3990     9.6537   0.974 0.330244    
## 2016 - 2007 == 0   1.3289     9.6537   0.138 0.890510    
## 2017 - 2007 == 0  16.2923     9.6537   1.688 0.091472 .  
## 2018 - 2007 == 0  17.7735     9.6537   1.841 0.065604 .  
## 2014 - 2010 == 0   3.0005     9.6537   0.311 0.755941    
## 2015 - 2010 == 0   4.4113     9.6537   0.457 0.647705    
## 2016 - 2010 == 0  -3.6588     9.6537  -0.379 0.704680    
## 2017 - 2010 == 0  11.3046     9.6537   1.171 0.241594    
## 2018 - 2010 == 0  12.7858     9.6537   1.324 0.185354    
## 2015 - 2014 == 0   1.4108     9.6537   0.146 0.883813    
## 2016 - 2014 == 0  -6.6594     9.6537  -0.690 0.490304    
## 2017 - 2014 == 0   8.3041     9.6537   0.860 0.389680    
## 2018 - 2014 == 0   9.7853     9.6537   1.014 0.310758    
## 2016 - 2015 == 0  -8.0701     9.6537  -0.836 0.403176    
## 2017 - 2015 == 0   6.8933     9.6537   0.714 0.475190    
## 2018 - 2015 == 0   8.3745     9.6537   0.867 0.385671    
## 2017 - 2016 == 0  14.9634     9.6537   1.550 0.121136    
## 2018 - 2016 == 0  16.4446     9.6537   1.703 0.088482 .  
## 2018 - 2017 == 0   1.4812     9.6537   0.153 0.878055    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Univariate p values reported)

2. Stacked categories - Supplement? Uva Island

Only plots, not stats

Explore 4x5

Data4_5<-subset(cover, Location=="4x5")

Explore Uva chains

Data_Chain_Uva<-subset(cover, Location=="UvRf-Chains")

By transect

Mean Chains

Uva_1m2

Data_Uva12<-subset(cover, Location=="Uva_1m2")

By transect

Mean 1m2

Cover<-grid.arrange(Plot_45 , Plot_UvaChains, Plot_Uva1m2, ncol=1)

#ggsave(file="Outputs/Fig_S1.svg", plot=Cover, width=8, height=10)

3. Supplemantary datasets (Canal del Afuera and Secas)

Import data

# Read Canal de Afuera data (Pocillopora 2014-2018) 
  Data_CanalAfuera <- read.csv("CoverData/CA_cover.csv", header=TRUE, sep = ",")
  #summary(Data_CanalAfuera)
  
# Read Secas data (Massives 1980-2018) 
  Data_Chain_SECAS <- read.csv("CoverData/Secas_cover.csv", header=TRUE, sep = ",")
  #summary(Data_Chain_SECAS)
  
  # Read Secas + Uva data (Massives 1980-2018) 
  Suplementary.masssives <- read.csv("CoverData/Massives_cover.csv", header=TRUE, sep = ",")
  #summary(Suplementary.masssives)
  
  
# Format color
  FILL <-c("#C77CFF", "#F8766D", "#00BA38", "#619CFF")

Pocillopora non-Uva (Canal de Afuera)

Pocillopora_CA <- ggplot(Data_CanalAfuera, aes(x=YEAR, y=Pocillopora)) +
  geom_boxplot(aes(group=YEAR), outlier.shape = NA) +
  stat_boxplot(aes(group=YEAR), geom = 'errorbar')+
  geom_point(colour="#A3A500", alpha=0.3)+
  stat_summary(fun.y=mean, geom="line", colour="#A3A500") +
  stat_summary(fun.y=mean, geom="point", shape=21, size=2, alpha=0.8, fill="#A3A500") +
  
  scale_y_continuous("Canal de afuera reef \n Pocillopora cover (%)", 
                     limits = c(-2, 90), breaks = seq(0, 100, by=20),
                     expand = c(0,0.1))+
  scale_x_continuous("", limits = c(1979, 2019),
                     breaks = seq(1980, 2018, by=2), expand = c(0,0))+
  facet_grid(Location~., scales="free")+
  
  ggtitle("a.")+
  
  annotate("rect", xmin = 1982, xmax = 1983, ymin = 0, ymax = 80,  alpha = .2, fill="gray")+
  annotate("rect", xmin = 1997, xmax = 1998, ymin = 0, ymax = 80,  alpha = .2, fill="gray")+
  annotate("rect", xmin = 2015, xmax = 2016, ymin = 0, ymax = 80,  alpha = .2, fill="gray")+
  facet_grid(Location~.)
Pocillopora_CA 

  • LMER model
  Data_CanalAfuera$Year_F<-as.factor(Data_CanalAfuera$YEAR)

  model_CA <- lme(
    Pocillopora ~ -1 + Year_F, random = ~1|Transect, data=Data_CanalAfuera)
  summary(model_CA)
## Linear mixed-effects model fit by REML
##   Data: Data_CanalAfuera 
##        AIC      BIC    logLik
##   114.7784 118.3186 -52.38918
## 
## Random effects:
##  Formula: ~1 | Transect
##         (Intercept) Residual
## StdDev:    9.232427 4.216186
## 
## Fixed effects:  Pocillopora ~ -1 + Year_F 
##               Value Std.Error DF  t-value p-value
## Year_F2015 57.43305  4.143548 10 13.86084       0
## Year_F2016 57.00977  4.143548 10 13.75868       0
## Year_F2018 70.15725  4.143548 10 16.93169       0
##  Correlation: 
##            Y_F2015 Y_F2016
## Year_F2016 0.827          
## Year_F2018 0.827   0.827  
## 
## Standardized Within-Group Residuals:
##         Min          Q1         Med          Q3         Max 
## -1.05091857 -0.65554034 -0.05954312  0.42760030  1.72437930 
## 
## Number of Observations: 18
## Number of Groups: 6
  anova(model_CA)
  plot(ranef(model_CA))    # Symmetrical scatter effects around zero?
  plot(model_CA)           # plot residuals vs fitted
  resnorm1 <- resid(model_CA)
  hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
  coef.m1 <- as.data.frame(coef(summary(model_CA)))    # Coefficients of the model
  
  plot(model_CA, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
  plot(model_CA, Pocillopora ~ fitted(.), abline = c(0,1))
  
# Multicomp
    Year_F.emm<-emmeans(model_CA, ~Year_F)
    #contrast(Year_F.emm, "tukey")
    year_groups<-cld(Year_F.emm, by=NULL) # compact-letter display
    year_groups
    #write.csv(year_groups, "Outputs/CanalPocilloTukey.csv", row.names = F)
    
# Effect plot
  plot(emmeans(model_CA, ~Year_F), comparisons = TRUE) +
      coord_flip(xlim = NULL, ylim = NULL, expand = TRUE) + theme_bw() +
    theme(axis.text.x = element_text(angle = 90)) + 
    ggtitle("Model CA preditions")

  • Summary stats Pocillopora CA

Massives Secas

Massive_Secas <- ggplot(Data_Chain_SECAS, aes(x=YEAR, y=Massive)) +
  geom_boxplot(aes(group=YEAR), outlier.shape = NA) +
  stat_boxplot(aes(group=YEAR), geom = 'errorbar')+
  #geom_smooth(method = lm, se=FALSE, linetype = "dashed", colour="red")+
  #geom_smooth(span = 0.2, se=T, colour="darkgray")+ 
  stat_summary(fun.y=mean, geom="line") +
  geom_point(aes(fill=Transect), alpha=0.5, shape=21) +
  
  scale_y_continuous("Secas Island reef \n Non-Pocillopora scleractinians cover (%)", 
                     limits = c(-2, 80), breaks = seq(0, 100, by=10),
                     expand = c(0,0.1)
                     )+
  scale_x_continuous("", limits = c(1979, 2019),
                     breaks = seq(1980, 2018, by=2)#, 
                     #expand = c(0.1,0)
                     )+
  annotate("rect", xmin = 1982, xmax = 1983, ymin = 0, ymax = 70,  alpha = .2, fill="gray")+
  annotate("rect", xmin = 1997, xmax = 1998, ymin = 0, ymax = 70,  alpha = .2, fill="gray")+
  annotate("rect", xmin = 2015, xmax = 2016, ymin = 0, ymax = 70,  alpha = .2, fill="gray")+
  #facet_grid(Location~., scales="free_y")
  ggtitle("b.")
Massive_Secas

  • LMER model SECAS
  Data_Chain_SECAS$Year_F<-as.factor(Data_Chain_SECAS$YEAR)

  model_Secas <- lme(
    Massive ~ -1 + Year_F, random = ~1|Transect, data=Data_Chain_SECAS)
  summary(model_Secas)
## Linear mixed-effects model fit by REML
##   Data: Data_Chain_SECAS 
##        AIC      BIC    logLik
##   1734.272 1796.924 -849.1361
## 
## Random effects:
##  Formula: ~1 | Transect
##          (Intercept) Residual
## StdDev: 0.0004912232 7.641786
## 
## Fixed effects:  Massive ~ -1 + Year_F 
##                Value Std.Error  DF   t-value p-value
## Year_F1975  1.891718  1.528357 231  1.237746  0.2171
## Year_F1976  0.898021  1.708755 231  0.525541  0.5997
## Year_F1977  1.621573  1.208273 231  1.342059  0.1809
## Year_F1978  1.679452  1.080712 231  1.554024  0.1215
## Year_F1980 18.183354  1.753146 231 10.371842  0.0000
## Year_F1983  0.385200  2.416545 231  0.159401  0.8735
## Year_F1997  0.225000  2.416545 231  0.093108  0.9259
## Year_F1998  0.904762  2.888324 231  0.313248  0.7544
## Year_F2000  0.000000  2.416545 231  0.000000  1.0000
## Year_F2002  0.158157  2.416545 231  0.065448  0.9479
## Year_F2003  0.500000  2.416545 231  0.206907  0.8363
## Year_F2004  0.300000  2.416545 231  0.124144  0.9013
## Year_F2005  0.200000  2.416545 231  0.082763  0.9341
## Year_F2010  1.200000  2.416545 231  0.496577  0.6200
## Year_F2015  0.264049  3.417511 231  0.077264  0.9385
## Year_F2018  0.070547  2.416545 231  0.029193  0.9767
##  Correlation: 
##            Y_F1975 Y_F1976 Y_F1977 Y_F1978 Y_F1980 Y_F1983 Y_F1997 Y_F1998
## Year_F1976 0                                                              
## Year_F1977 0       0                                                      
## Year_F1978 0       0       0                                              
## Year_F1980 0       0       0       0                                      
## Year_F1983 0       0       0       0       0                              
## Year_F1997 0       0       0       0       0       0                      
## Year_F1998 0       0       0       0       0       0       0              
## Year_F2000 0       0       0       0       0       0       0       0      
## Year_F2002 0       0       0       0       0       0       0       0      
## Year_F2003 0       0       0       0       0       0       0       0      
## Year_F2004 0       0       0       0       0       0       0       0      
## Year_F2005 0       0       0       0       0       0       0       0      
## Year_F2010 0       0       0       0       0       0       0       0      
## Year_F2015 0       0       0       0       0       0       0       0      
## Year_F2018 0       0       0       0       0       0       0       0      
##            Y_F2000 Y_F2002 Y_F2003 Y_F2004 Y_F2005 Y_F2010 Y_F2015
## Year_F1976                                                        
## Year_F1977                                                        
## Year_F1978                                                        
## Year_F1980                                                        
## Year_F1983                                                        
## Year_F1997                                                        
## Year_F1998                                                        
## Year_F2000                                                        
## Year_F2002 0                                                      
## Year_F2003 0       0                                              
## Year_F2004 0       0       0                                      
## Year_F2005 0       0       0       0                              
## Year_F2010 0       0       0       0       0                      
## Year_F2015 0       0       0       0       0       0              
## Year_F2018 0       0       0       0       0       0       0      
## 
## Standardized Within-Group Residuals:
##          Min           Q1          Med           Q3          Max 
## -2.379463717 -0.212198142 -0.075570702 -0.004047582  6.834475873 
## 
## Number of Observations: 256
## Number of Groups: 10
  anova(model_Secas)
  plot(ranef(model_Secas))    # Symmetrical scatter effects around zero?
  plot(model_Secas)           # plot residuals vs fitted
  resnorm1 <- resid(model_Secas)
  hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
  coef.m1 <- as.data.frame(coef(summary(model_Secas)))    # Coefficients of the model
  
  plot(model_Secas, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
  plot(model_Secas, Pocillopora ~ fitted(.), abline = c(0,1))
  
# Multicomp
    Year_F.emm<-emmeans(model_Secas, ~Year_F)
    #contrast(Year_F.emm, "tukey")
    year_groups<-cld(Year_F.emm, by=NULL) # compact-letter display
    year_groups 
    #write.csv(year_groups, "Outputs/SecasNonPocilloTukey.csv", row.names = F)
    
# Effect plot
  plot(emmeans(model_Secas, ~Year_F), comparisons = TRUE) +
      coord_flip(xlim = NULL, ylim = NULL, expand = TRUE) + theme_bw() +
    theme(axis.text.x = element_text(angle = 90)) + 
    ggtitle("Model Secas preditions")

  • Summary stats Massives Secas

Massives Uva+Secas

Other Supplemetary figures cover

Packages used

Auguie, Baptiste. 2017. GridExtra: Miscellaneous Functions for "Grid" Graphics. https://CRAN.R-project.org/package=gridExtra.

Genz, Alan, and Frank Bretz. 2009. Computation of Multivariate Normal and T Probabilities. Lecture Notes in Statistics. Heidelberg: Springer-Verlag.

Genz, Alan, Frank Bretz, Tetsuhisa Miwa, Xuefei Mi, and Torsten Hothorn. 2021. Mvtnorm: Multivariate Normal and T Distributions. http://mvtnorm.R-forge.R-project.org.

Hothorn, Torsten. 2019. TH.data: TH’s Data Archive. https://CRAN.R-project.org/package=TH.data.

Hothorn, Torsten, Frank Bretz, and Peter Westfall. 2008. “Simultaneous Inference in General Parametric Models.” Biometrical Journal 50 (3): 346–63.

———. 2021. Multcomp: Simultaneous Inference in General Parametric Models. https://CRAN.R-project.org/package=multcomp.

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